Once the gain and crossover is set properly, there is no need to touch the amp for the sub anymore. And I believe the remote line is to adjust the gain so you should be good.

I used one amp for the sub and one for the speakers. I ran RCAs from the back of the radio to the amps in the back. I already had the premium system so all the speaker wires were already back there, battery was right there too.

I never actually tested the factory sub correctly, I just followed another users suggestion and purchased the 8” Dayton audio subwoofer. It is very cheap, so I thought it would be better to put in new. Maybe someone else can answer that one, it might be fine with the new amp and factory sub?