Goin'Sideways

Hey guys, hope you guys can help me with my problem:

So i just bought a 1999 Trans Am WS6, had it shipped up from California (i live around Seattle, WA), picked it up from the shippers and drove it home. When I got home, i started futzing with the custom security system remote. I somehow armed the system, and so every time i would open a door or try to start the car, the alarm would go off (and wouldn't let me turn the car on). I tried every possible combination of button pushing, and nothing would work. Also went online and tried some things, but still no luck. So i called the guy who I bought it from, and he walked me through a few steps of undoing the battery, re-connecting the battery, and messing with some switches. That not working, he then walked me through finding a box under the dash (he said it had a fuse on it) which had a plug in it. I couldn't find it, so I said I'd futs around with it some more.

So in the morning i went back out, found the box, and pulled the plug (which had a bunch of wires attached to it). The alarm went off, but when i tried to start the car, all the lights would go off, and nothing would happen, so i assumed the battery was dead. So i got another car, hooked the jump-starting cables, started the other car, and then tried to start the Trans am. Same thing happened, all lights went off, all gauges went off, and nothing happened.

So i messed around with taking the negative terminal on and off from the battery, and seeing if i had incorrectly screwed the cord onto the battery (i had noticed the day before that when i was screwing in the cord to the battery, it would sometimes act as if the power was fluctuating, and the car alarm would go on and off rapidly). So after repeating the jump starting and futzing with the battery, it eventually got to the point of where when i turned the car on, the little dinger thingy that lets you know the keys are in the ignition would make a eh eh eh eh eh sound, instead of the longer ding it normally does. Then when I'm screwing the negative terminal back into the battery, i hear weird tapping noises by the passenger's side by the window. I would also hear a weird sound coming from one of the fuse boxes, and one from the front of the engine towards the bottom. I then re-plugged the plug that i pulled from (what i thought was) the alarm box thingy to make sure i hadn't pulled the wrong plug, and the siren went on, but sounded like it was constantly being interrupted every 1/4 of a second like the key dinger inside the car was.

So i'm wondering, have i totally screwed up the battery by bolting and un-bolting the terminal (i'm not sure if that is the right name for that black cord...) too many times, or have I blown a fuse or what? (btw, sorry for the long post, just figured that the more info i put on what happened, the easier it would be to identify the problem.

Hope you guys know what is going on!