Stereo Upgrade Question - Wire Size for Aftermarket Amplifier
07-25-2012, 08:56 PM
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Staging Lane
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Stereo Upgrade Question - Wire Size for Aftermarket Amplifier Hi All!
I am upgrading my stereo system and wanted to get a bit of advice? I think I'm going full rewire - but wanted to ask the pros before I start making with the alterations. I've got an 02 WS6.
What I've already done:
1. Replaced factory head unit with aftermarket Pioneer (7000BT)
2. Added the PAC steering wheel controls
3. Replaced door and sailfin speakers (with polks)
4. Added a JLAudio Stealthbox to Driver Side
(Stealthbox is running a 10" MTX sub on a Sony Xplod amp I poached from my dad)
Assessment - It's not loud enough. (hang head in shame)
So I have another aftermarket (sony xplod) amplifier that I've been carrying around (again, courtesy of dad) - and think I'm ready to get after replacing that monsoon amp. I've tried it - upgraded everything else and still want more volume.
So - I've got 2 more sets of RCA outputs off the back of my pioneer that I can run back there to the aftermarket amp. (4 channel amp) I've already put in the 0 gauge power to the back with the inline fuse. I believe the junction I put in at the back splits to 4 or 8 gauge wire. Can't remember - but I know I was planning on needing to run 2 amps back there and expect I would have gone with a bigger wire.
Question #1:
What gauge wire would you guys recommend to run for the new speaker wires? I see notes about the stock wiring being a little small.
My theory is that I'll run wires for the doors and the sailfin speakers and tie those to the new amplifier - but open to suggestions.
Question #2:
Any value in leaving the monsoon there to run other speakers?
***part B: if so, which speakers are best to run on the monsoon?
I *THINK* that my head unit will allow me to use the speaker level wires and the RCAs because I'm currently using the RCA for my sub and the factory harness for the rest of the system. I read something about there being a center channel in the dash with the monsoon that you lose if you take that out - but am a little confused as to if I actually have one or not. (I thought I only had 10 speakers) I may have misunderstood this.
Question #3: What about adding adapter harnesses for the speakers?
Thinking ahead that I'll be playing with the speakers in there - and always love that I can unplug them and haul them into my apartment to solder the connections - then take them back down for a quick plug and play. Are there any out there that you would recommend using? Or do you vote to reuse the ones existing in the car? (I was trying to leave as much intact as possible - even if the factory adapters off the speakers just sort of live in a ziplock bag for possible future use) Am I overly respectful about trying not to modify the factory wiring?
I just did the passenger door window fix (autotrix) so I've got everything opened up to get into that boot again if I run wires.
Oh - also, I haven't gotten to put it in yet - because it won't stop RAINING - but I've picked up a WAI Transpo 253 amp alternator (it's GORGEOUS!! the 2003 truck housing) and the wiring to do the Big 3(4). So I'm expecting that I'd have enough power to leave the monsoon in there if it's a good choice. Feel free (please) school me if I'm wrong.
Thanks so much in advance for sharing the intel!!
I am upgrading my stereo system and wanted to get a bit of advice? I think I'm going full rewire - but wanted to ask the pros before I start making with the alterations. I've got an 02 WS6.
What I've already done:
1. Replaced factory head unit with aftermarket Pioneer (7000BT)
2. Added the PAC steering wheel controls
3. Replaced door and sailfin speakers (with polks)
4. Added a JLAudio Stealthbox to Driver Side
(Stealthbox is running a 10" MTX sub on a Sony Xplod amp I poached from my dad)
Assessment - It's not loud enough. (hang head in shame)
So I have another aftermarket (sony xplod) amplifier that I've been carrying around (again, courtesy of dad) - and think I'm ready to get after replacing that monsoon amp. I've tried it - upgraded everything else and still want more volume.
So - I've got 2 more sets of RCA outputs off the back of my pioneer that I can run back there to the aftermarket amp. (4 channel amp) I've already put in the 0 gauge power to the back with the inline fuse. I believe the junction I put in at the back splits to 4 or 8 gauge wire. Can't remember - but I know I was planning on needing to run 2 amps back there and expect I would have gone with a bigger wire.
Question #1:
What gauge wire would you guys recommend to run for the new speaker wires? I see notes about the stock wiring being a little small.
My theory is that I'll run wires for the doors and the sailfin speakers and tie those to the new amplifier - but open to suggestions.
Question #2:
Any value in leaving the monsoon there to run other speakers?
***part B: if so, which speakers are best to run on the monsoon?
I *THINK* that my head unit will allow me to use the speaker level wires and the RCAs because I'm currently using the RCA for my sub and the factory harness for the rest of the system. I read something about there being a center channel in the dash with the monsoon that you lose if you take that out - but am a little confused as to if I actually have one or not. (I thought I only had 10 speakers) I may have misunderstood this.
Question #3: What about adding adapter harnesses for the speakers?
Thinking ahead that I'll be playing with the speakers in there - and always love that I can unplug them and haul them into my apartment to solder the connections - then take them back down for a quick plug and play. Are there any out there that you would recommend using? Or do you vote to reuse the ones existing in the car? (I was trying to leave as much intact as possible - even if the factory adapters off the speakers just sort of live in a ziplock bag for possible future use) Am I overly respectful about trying not to modify the factory wiring?
I just did the passenger door window fix (autotrix) so I've got everything opened up to get into that boot again if I run wires.
Oh - also, I haven't gotten to put it in yet - because it won't stop RAINING - but I've picked up a WAI Transpo 253 amp alternator (it's GORGEOUS!! the 2003 truck housing) and the wiring to do the Big 3(4). So I'm expecting that I'd have enough power to leave the monsoon in there if it's a good choice. Feel free (please) school me if I'm wrong.
Thanks so much in advance for sharing the intel!!
07-26-2012, 01:31 AM
#2
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Its been a few years since I have really messed around with car audio (how ever long ago Circuit City closed) other than a simple speaker door speaker install, remote start/alarm and a double din in my silverado. But if I am wrong about anything I'm sure someone will correct me.
Question #1:
What gauge wire would you guys recommend to run for the new speaker wires?
Typically you dont need to upgrade the stock wire, most speakers you are using are not going to be pulling so much power to were you will be melting wires.
If you are going with the 4 channel the easiest and cleanest install is to take all 4 sets of wires to the back of the head unit and cut the wires between the radio and the speakers and make your connections there, rather than fishing wire through all the panels and under the carpet etc.
Question #2:
Any value in leaving the monsoon there to run other speakers?
The stock amp is typically bypassed... but you mentioned you had a 4channel you were going to run so you will want to bypass the monsoon amp anyway.
***part B: if so, which speakers are best to run on the monsoon?
If you wanted to run speakers off the monsoon you need to find the correct ohm speakers for the monsoon amp. (which I believe was 2 ohms)
I could be wrong once again but I thought there was only 6? (someone else chime in here) Its been awhile since I have done any stereo mods in a camaro at all.
Question #3: What about adding adapter harnesses for the speakers?
Go for it. They are really nice and it beats having to splice into the factory harness. (most people like to just cut the old harness off and toss it away and you can never return it back to stock if you wanted too, if you dont use the speaker harness just strip back a little wire behind the factory harness and tap into it.)
When I do car audio I tend to get rid of all the stock traces of everything. I had bose in my truck, im running 6 1/2 focal access components up front, polk 4x6s in the rear, JL 300/4 pushing those, I had a JL 10W3 v2 ran by a JL 250/1 but I didnt like having a box just sitting on the seat (I pulled it out the camaro after it got flooded out) The next thing I am going to do is build a custom box and stuff a JL 8W7 under the rear seat.
As for what guage wires to run... being sony amps... just run 8 off the dist block. And if you want to run wire to all your speakers/or even from the amp to the back of the radio to use the factory wires (what I would do) just the normal old clear jacked 18 gauge wire will be fine. you can use 16-14 if you want. 12 gauge for subs.
-Cowboy
Question #1:
What gauge wire would you guys recommend to run for the new speaker wires?
Typically you dont need to upgrade the stock wire, most speakers you are using are not going to be pulling so much power to were you will be melting wires.
If you are going with the 4 channel the easiest and cleanest install is to take all 4 sets of wires to the back of the head unit and cut the wires between the radio and the speakers and make your connections there, rather than fishing wire through all the panels and under the carpet etc.
Question #2:
Any value in leaving the monsoon there to run other speakers?
The stock amp is typically bypassed... but you mentioned you had a 4channel you were going to run so you will want to bypass the monsoon amp anyway.
***part B: if so, which speakers are best to run on the monsoon?
If you wanted to run speakers off the monsoon you need to find the correct ohm speakers for the monsoon amp. (which I believe was 2 ohms)
I could be wrong once again but I thought there was only 6? (someone else chime in here) Its been awhile since I have done any stereo mods in a camaro at all.
Question #3: What about adding adapter harnesses for the speakers?
Go for it. They are really nice and it beats having to splice into the factory harness. (most people like to just cut the old harness off and toss it away and you can never return it back to stock if you wanted too, if you dont use the speaker harness just strip back a little wire behind the factory harness and tap into it.)
When I do car audio I tend to get rid of all the stock traces of everything. I had bose in my truck, im running 6 1/2 focal access components up front, polk 4x6s in the rear, JL 300/4 pushing those, I had a JL 10W3 v2 ran by a JL 250/1 but I didnt like having a box just sitting on the seat (I pulled it out the camaro after it got flooded out) The next thing I am going to do is build a custom box and stuff a JL 8W7 under the rear seat.
As for what guage wires to run... being sony amps... just run 8 off the dist block. And if you want to run wire to all your speakers/or even from the amp to the back of the radio to use the factory wires (what I would do) just the normal old clear jacked 18 gauge wire will be fine. you can use 16-14 if you want. 12 gauge for subs.
-Cowboy
07-26-2012, 08:55 AM
#3
Sorry, but I'm afraid I can't agree with parts of the previous post. I'm a firm believer that doing upgrades to a stock system should be done with plug-in adapters to the factory wiring (head unit and speakers). But if you're going to revamp the whole system with an aftermarket amp (or two) then you should leave the factory wiring alone and run all your own wiring. The very thought of running the output of an amp to the back of the head unit and then cutting and splicing into the factory wiring makes me very glad I never went to CC (or BB) for any installations.
One reason to run your own wiring is for practicality - running RCAs to an amp that is mounted at the back of the car doesn't lend itself to then connecting the output back to the speakers through the factory wiring. Another reason is that when you spend some serious money on an audio system, you may want to take it with you to another car so leaving the factory wiring completely intact allows you to return the car to stock when selling. And finally, judging by your quest for more volume, you probably want to run larger wire than stock.
Question #1 - I suggest 16 gauge unless you expect to send more than 250 watts into 4 ohms to each speaker. 16 gauge is small and flexible enough to be easy to install but big enough to handle the current of some pretty big amps. If you keep it down to less than 100 watts per channel into 4-ohms, you can even use 18 gauge wire without worrying about signal loss. If you use 2-ohm speakers and/or run more than 250 watts per channel, you'll have to go up to 14 gauge. And if you go as big as 1,000 watts for the sub, you'll need 12 gauge. All of this is based on power (watts), speaker impedance, and the length of wire with less than 1dB of signal loss.
Question #2 - You have ten speakers in six locations in your Firebird (Camaros have eight speakers in six locations) but they were originally set up with very specific speaker types in certain locations (e.g. subs in the sail panels). You have replaced the doors and sails with full-range speakers so you should not have any need for the only remaining stock location - the hatch area speakers. The hatch speakers were originally there for full-range rear fill audio. Since you will already have full-range sound behind you (the new sail panel speakers), it is not a good idea to add even more high frequencies in the back of the car. That would move the sound stage too far back and make it seem like a 60s car with all the sound coming from 6x9 speakers in the rear parcel panel. I recommend leaving the hatch speakers disconnected (the mids back there run off the amp but the tweeters run directly off the head unit).
Question #3 - Since you won't be using the factory wiring, this is a moot question. Simply put quick connect terminals on the ends of the new wire you run and you will be able unplug your speakers without a need for specific adapters. Leave the factory wiring intact so you can easily go back to stock if you decide to sell the car and take your audio system out.
One reason to run your own wiring is for practicality - running RCAs to an amp that is mounted at the back of the car doesn't lend itself to then connecting the output back to the speakers through the factory wiring. Another reason is that when you spend some serious money on an audio system, you may want to take it with you to another car so leaving the factory wiring completely intact allows you to return the car to stock when selling. And finally, judging by your quest for more volume, you probably want to run larger wire than stock.
Question #1 - I suggest 16 gauge unless you expect to send more than 250 watts into 4 ohms to each speaker. 16 gauge is small and flexible enough to be easy to install but big enough to handle the current of some pretty big amps. If you keep it down to less than 100 watts per channel into 4-ohms, you can even use 18 gauge wire without worrying about signal loss. If you use 2-ohm speakers and/or run more than 250 watts per channel, you'll have to go up to 14 gauge. And if you go as big as 1,000 watts for the sub, you'll need 12 gauge. All of this is based on power (watts), speaker impedance, and the length of wire with less than 1dB of signal loss.
Question #2 - You have ten speakers in six locations in your Firebird (Camaros have eight speakers in six locations) but they were originally set up with very specific speaker types in certain locations (e.g. subs in the sail panels). You have replaced the doors and sails with full-range speakers so you should not have any need for the only remaining stock location - the hatch area speakers. The hatch speakers were originally there for full-range rear fill audio. Since you will already have full-range sound behind you (the new sail panel speakers), it is not a good idea to add even more high frequencies in the back of the car. That would move the sound stage too far back and make it seem like a 60s car with all the sound coming from 6x9 speakers in the rear parcel panel. I recommend leaving the hatch speakers disconnected (the mids back there run off the amp but the tweeters run directly off the head unit).
Question #3 - Since you won't be using the factory wiring, this is a moot question. Simply put quick connect terminals on the ends of the new wire you run and you will be able unplug your speakers without a need for specific adapters. Leave the factory wiring intact so you can easily go back to stock if you decide to sell the car and take your audio system out.
07-26-2012, 10:44 AM
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Sorry, but I'm afraid I can't agree with parts of the previous post. I'm a firm believer that doing upgrades to a stock system should be done with plug-in adapters to the factory wiring (head unit and speakers). But if you're going to revamp the whole system with an aftermarket amp (or two) then you should leave the factory wiring alone and run all your own wiring. The very thought of running the output of an amp to the back of the head unit and then cutting and splicing into the factory wiring makes me very glad I never went to CC (or BB) for any installations.
But as far as everything else goes you know way more on the subject of the f body audio system. I had a 95 LT1 wasnt much to it as far as nice audio. 4 speaks and that was it.
07-26-2012, 10:56 AM
#5
Like in most professions, there are some installers that take shortcuts for expediency and some that try to do things right whenever possible. Nice to hear you are one of the latter. Unfortunately, the big box stores tend to have a lot of the former.
07-26-2012, 01:57 PM
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Alright - Good to go! Thanks a bunch!!
So now I'm off to the store to get some 14 gauge and quick connects. I'm pretty sure I've worked with the 16 and 18 before - I believe that's what I've used rewiring lamps and chandeliers? Those are easy to work with - so figure I'll go ahead and step up to the 14 *just in case*. I'm betting that I'd want a bigger amp before I'd sell the car - so may as well run the big stuff now rather than have to redo it later. (it's my second firebird - had a 94 formula before this one. These cars are "home" for me. I foresee many more happy years of engine mods together)
White Bird - do you have a suggestion as to which path to run the wire to get to the driver side? I've tried to keep RCAs running down the passenger side - and my power running down the drivers side. That seemed to be how it was originally run. I've got a big 0 gauge wire running down the driver side to the sub in the back.
I have respect for those wires and not getting power too close to signal. Learned the hard way that when those wires shift together too close my subwoofer comes off the hinges so loud I pull off the road like a crazy person to get out of the car and figure out how to turn it off. So I've got power under the carpet at the seam where the hatch drops off into the t-top well - and the speaker wire at the bottom of the well under the carpet. Ha - maybe I should add one of those little subwoofer volume switches under the dash too.
So about that wiring path - passenger door and sail fin are easy enough to run up the side. Should I take the wires across under the dash to get around to the driver side door? What about the driver side sailfin? Any path under the seat, etc? Is there something I should do to shield it from the power running down that side? Or am I being paranoid? (sub incident scared me for life)
Oh and thanks for the confirmation on the 10 speaker count. I was surprised to read that about a center channel in the dash - but then figured I get schooled on things I didn't know about my car all the time. Maybe they were talking about an earlier year fb. (or maybe they were dead wrong - ha!) I've had mine out so many times - I'll buy a set off Craigslist and pop them in - see which I like better. Was going to be embarrassed if I'd missed one.
So now I'm off to the store to get some 14 gauge and quick connects. I'm pretty sure I've worked with the 16 and 18 before - I believe that's what I've used rewiring lamps and chandeliers? Those are easy to work with - so figure I'll go ahead and step up to the 14 *just in case*. I'm betting that I'd want a bigger amp before I'd sell the car - so may as well run the big stuff now rather than have to redo it later. (it's my second firebird - had a 94 formula before this one. These cars are "home" for me. I foresee many more happy years of engine mods together)
White Bird - do you have a suggestion as to which path to run the wire to get to the driver side? I've tried to keep RCAs running down the passenger side - and my power running down the drivers side. That seemed to be how it was originally run. I've got a big 0 gauge wire running down the driver side to the sub in the back.
I have respect for those wires and not getting power too close to signal. Learned the hard way that when those wires shift together too close my subwoofer comes off the hinges so loud I pull off the road like a crazy person to get out of the car and figure out how to turn it off.
So I've got power under the carpet at the seam where the hatch drops off into the t-top well - and the speaker wire at the bottom of the well under the carpet. Ha - maybe I should add one of those little subwoofer volume switches under the dash too. So about that wiring path - passenger door and sail fin are easy enough to run up the side. Should I take the wires across under the dash to get around to the driver side door? What about the driver side sailfin? Any path under the seat, etc? Is there something I should do to shield it from the power running down that side? Or am I being paranoid? (sub incident scared me for life)
Oh and thanks for the confirmation on the 10 speaker count. I was surprised to read that about a center channel in the dash - but then figured I get schooled on things I didn't know about my car all the time. Maybe they were talking about an earlier year fb. (or maybe they were dead wrong - ha!) I've had mine out so many times - I'll buy a set off Craigslist and pop them in - see which I like better. Was going to be embarrassed if I'd missed one.
07-26-2012, 02:02 PM
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White Bird - one more thought? I'm not married to those polks. I've been thinking about putting some subs in the back seat - maybe the bazookas. (got more research to do there)
I definitely like the "full" sound - don't want too many high notes. Starts to sound "tinny". Have you ever heard of anyone sneaking in a pair of 8" subs back there or is that too much with the 10" in the back and sticking to the 6" subs is better? Or do you recommend the full range? I think the polks I have may only be 2 way... I want to say they're 6 3/4 DBLs? (I could be wrong on that one) But I figure they're only putting out the signal that the monsoon currently sends them so I'm not sure what I'm in for once I get the amps switched out.
Also - should I just disconnect the factory speaker harness from the head unit? Or do I need to leave that for the remote wire/antenna?
Thanks again!!!!
I definitely like the "full" sound - don't want too many high notes. Starts to sound "tinny". Have you ever heard of anyone sneaking in a pair of 8" subs back there or is that too much with the 10" in the back and sticking to the 6" subs is better? Or do you recommend the full range? I think the polks I have may only be 2 way... I want to say they're 6 3/4 DBLs? (I could be wrong on that one) But I figure they're only putting out the signal that the monsoon currently sends them so I'm not sure what I'm in for once I get the amps switched out.
Also - should I just disconnect the factory speaker harness from the head unit? Or do I need to leave that for the remote wire/antenna?
Thanks again!!!!
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07-26-2012, 03:41 PM
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Using shielded RCA cables in combination with a HU that has 4-5V RCA outputs should alleviate any noise issues, even if you run them with the power cables. Keeping power and speaker wires away from your RCAs would be ideal, though.
https://ls1tech.com/forums/ls1-domes...t-1478525.html
https://ls1tech.com/forums/ls1-domes...t-1400982.html
https://ls1tech.com/forums/ls1-domes...t-1478525.html
https://ls1tech.com/forums/ls1-domes...t-1400982.html
07-26-2012, 03:50 PM
#9
Lots of questions... let me know if I miss something.
Wiring path: You have a couple of options but the one that may work best for you (since you profess to being paranoid about running wires together) is to run power down one side, input signal (RCAs) down the other side and output signal (to speakers) up the middle under the center console. In general, it's not good to run power and signal wires together parallel to each other but it is not a problem to have signal wires cross over power wires (perpendicular). That's how you avoid problems with running signal to speakers that are on the side of the car where you have your power wires.
Sail panel subs: Personally, I like having the mid-bass speakers in the sail panels (6.5" is too small to be a true sub) because it adds to the richness of the sound and doesn't detract from the front sound stage. However, I also like rear fill for that surround sound feeling so I would leave the hatch speakers connected if you use subs in the sail panels. Right now your full-range Polks are acting as mid-bass only because that's all the signal they get from the Monsoon amp. Once you switch to your own amp, they will get unfiltered signal and your overall balance of treble to bass will go up significantly. That would not be my first choice but some people like it. If you decide to use 6.5" subs with your new amp then make sure you get low pass filters to prevent high frequency signal reaching them.
I have seen f-bodies that have had the sail panels hacked to fit 8" subs and it can work quite well depending on what you want. However, I expect it would make your music somewhat bass heavy when combined with a 10" stealthbox sub.
Harness: You're going to need the factory harness adapter connected to your aftermarket head unit for power, ground, steering wheel controls, power antenna, illumination, etc. so disconnecting the speakers is not really an option. Besides, it won't affect anything since your speakers will be powered by your new amp through your own wiring and it also gives you the option to leave the hatch speakers connected to the Monsoon amp if you decide to go with sail panel subs.
Wiring path: You have a couple of options but the one that may work best for you (since you profess to being paranoid about running wires together) is to run power down one side, input signal (RCAs) down the other side and output signal (to speakers) up the middle under the center console. In general, it's not good to run power and signal wires together parallel to each other but it is not a problem to have signal wires cross over power wires (perpendicular). That's how you avoid problems with running signal to speakers that are on the side of the car where you have your power wires.
Sail panel subs: Personally, I like having the mid-bass speakers in the sail panels (6.5" is too small to be a true sub) because it adds to the richness of the sound and doesn't detract from the front sound stage. However, I also like rear fill for that surround sound feeling so I would leave the hatch speakers connected if you use subs in the sail panels. Right now your full-range Polks are acting as mid-bass only because that's all the signal they get from the Monsoon amp. Once you switch to your own amp, they will get unfiltered signal and your overall balance of treble to bass will go up significantly. That would not be my first choice but some people like it. If you decide to use 6.5" subs with your new amp then make sure you get low pass filters to prevent high frequency signal reaching them.
I have seen f-bodies that have had the sail panels hacked to fit 8" subs and it can work quite well depending on what you want. However, I expect it would make your music somewhat bass heavy when combined with a 10" stealthbox sub.
Harness: You're going to need the factory harness adapter connected to your aftermarket head unit for power, ground, steering wheel controls, power antenna, illumination, etc. so disconnecting the speakers is not really an option. Besides, it won't affect anything since your speakers will be powered by your new amp through your own wiring and it also gives you the option to leave the hatch speakers connected to the Monsoon amp if you decide to go with sail panel subs.
07-28-2012, 01:37 AM
#10
Lots of questions... let me know if I miss something.
Wiring path: You have a couple of options but the one that may work best for you (since you profess to being paranoid about running wires together) is to run power down one side, input signal (RCAs) down the other side and output signal (to speakers) up the middle under the center console. In general, it's not good to run power and signal wires together parallel to each other but it is not a problem to have signal wires cross over power wires (perpendicular). That's how you avoid problems with running signal to speakers that are on the side of the car where you have your power wires.
Sail panel subs: Personally, I like having the mid-bass speakers in the sail panels (6.5" is too small to be a true sub) because it adds to the richness of the sound and doesn't detract from the front sound stage. However, I also like rear fill for that surround sound feeling so I would leave the hatch speakers connected if you use subs in the sail panels. Right now your full-range Polks are acting as mid-bass only because that's all the signal they get from the Monsoon amp. Once you switch to your own amp, they will get unfiltered signal and your overall balance of treble to bass will go up significantly. That would not be my first choice but some people like it. If you decide to use 6.5" subs with your new amp then make sure you get low pass filters to prevent high frequency signal reaching them.
I have seen f-bodies that have had the sail panels hacked to fit 8" subs and it can work quite well depending on what you want. However, I expect it would make your music somewhat bass heavy when combined with a 10" stealthbox sub.
Harness: You're going to need the factory harness adapter connected to your aftermarket head unit for power, ground, steering wheel controls, power antenna, illumination, etc. so disconnecting the speakers is not really an option. Besides, it won't affect anything since your speakers will be powered by your new amp through your own wiring and it also gives you the option to leave the hatch speakers connected to the Monsoon amp if you decide to go with sail panel subs.
Wiring path: You have a couple of options but the one that may work best for you (since you profess to being paranoid about running wires together) is to run power down one side, input signal (RCAs) down the other side and output signal (to speakers) up the middle under the center console. In general, it's not good to run power and signal wires together parallel to each other but it is not a problem to have signal wires cross over power wires (perpendicular). That's how you avoid problems with running signal to speakers that are on the side of the car where you have your power wires.
Sail panel subs: Personally, I like having the mid-bass speakers in the sail panels (6.5" is too small to be a true sub) because it adds to the richness of the sound and doesn't detract from the front sound stage. However, I also like rear fill for that surround sound feeling so I would leave the hatch speakers connected if you use subs in the sail panels. Right now your full-range Polks are acting as mid-bass only because that's all the signal they get from the Monsoon amp. Once you switch to your own amp, they will get unfiltered signal and your overall balance of treble to bass will go up significantly. That would not be my first choice but some people like it. If you decide to use 6.5" subs with your new amp then make sure you get low pass filters to prevent high frequency signal reaching them.
I have seen f-bodies that have had the sail panels hacked to fit 8" subs and it can work quite well depending on what you want. However, I expect it would make your music somewhat bass heavy when combined with a 10" stealthbox sub.
Harness: You're going to need the factory harness adapter connected to your aftermarket head unit for power, ground, steering wheel controls, power antenna, illumination, etc. so disconnecting the speakers is not really an option. Besides, it won't affect anything since your speakers will be powered by your new amp through your own wiring and it also gives you the option to leave the hatch speakers connected to the Monsoon amp if you decide to go with sail panel subs.
