Which O2's to use?
 

Do i use the sensors off the manifolds or off the cat and lower y-pipe which have square plugs? What will i need to do with the plugs that used to connect into the manifolds, can i just leave em?

The sensors after the cats are catalyst efficiency monitors. If they're throwing codes either replace the cats or gut the cats and get o2 sims. The manifold sensors are the ones that actually adjust the air fuel ratio and are important to proper engine operation.

ok, so i put the wrong O2's in my LT's? I need to put the manifold sensors in my LT's?

yes. that is correct.

good to know.....how should i route the extensions so they dont rub the ground or hit the headers? Can i zip-tie them to the transmission or will the tranny get to hot?

I'd try to zip tie them against something other than the tranny. If the extensions have a lot of slack zip tie them to the body.

sounds good,