My question is if I use the high level input when installing can I use the wires that plug into the factory subwoofer? Keep in mind that this signal would be filtered through the factory crossover and amp at this point. Would that matter? If it does, does anyone know what wires I can tap into pre-factory amp?

 

depends on what you want the amp to power.

if you want the amp with high level inputs to power a sub, tapping the factory sub speaker wires is a good idea - but remember two things,
1. you need to disconnect the ANC system microphones.
2. you should remove the factory sub completely.

if you want the amp with high level inputs to power speakers, tap the factory wires that feed the speakers you are replacing (front or rear).

 

you dont want to put a aftermarket system its a hassle only cause of the mics in the car there two one in the front and in the rear

 

bypassing the mics is fairly straightforward.