I think I know where you are confused. I'll do my best to explain all this. I have a simular set up in my car, but a previous owner set it all up. So here goes...
When you hook up a head unit to an amp your not using the amp in the HU therefore your not going to use the speaker output from the HU. The RCA connections on the back of the HU are "pre-outs", meaning pre-amplified. The 2 RCA connections on the back of the HU should be labled "Front" and "Rear" So your gong to want to run 2 RCA cables from that connection to your amp then run speaker wire from the amp to the speakers. The rear speakers are the easy ones. I am not clear on how the front speakers are connected since there is one in the dash and one in the door. I am not sure where the previous owner tapped into the front speakers with the speaker wires from the amp in my car. I have heard they are wired in parallel, but I am not sure of that, Power would be able to help you there. I hope this has helped. If you need a diagram I think can throw one together pretty quick.
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