If your deck has RCAs outputs use rca cables and route them to the amp from the deck. Then speaker wires go from the amp to the speakers. If it doesnt have rca outputs, then run wires from the two back door speakers to the speaker level inputs at the amp. If the aftermarket amp is going to power the door speakers, then just dissconnect the factory amp and run wire from the aftermarket amp to the door speakers. If it is going to power subwoofers, then run wires from the aftermarket amp to the subs. I dont see any problem with using the factory amp in its original setup to power the door speakers if the aftermarket amp is powering something else, like subs. Dont use both amps to power the same speakers.Hope this helps.