Lol ok so you got two 2 channel amps, one is dedicated to your sub while the other is for mids/highs correct?

Alrighty if so just hook up your mids/highs amp to your Front/Rear pre-outs (RCA's) while your sub amp shall go to the sub pre-outs. This is so you have control of your sub's output from the deck along with its EQ/fader properties. Simple right?