yep you'll have to bypass the amp to make the cars stock wiring work, but when i did mine i figured i had to tear the car all apart to run the other wires and the stock ones are kinda small so i ran new speaker wire to all the speakers right from the amp. my hu has three sets of preouts so i didnt fool with the stock amp wiring just bypassed it all together. they do have premade bypass harnesses for some cars if you want to go that way.
i went with two amps too like mouse said, and its hard to find exactly what you want unless you want to really pay for it. and say you want to change to a different sub or whatever your locked in because you dont want to have to pay all that money again
1998 Bonneville SSE
2007 Monte Carlo LT-KYB, Clarion, Polk audio, Kicker
1999 Yukon SLE-KYB, Air lift, Reese dual-cam, Tekonsha
1987 Firebird-355/th400-nothing stock