I have an aftermarket deck installed. I am not positive how to go about getting the RCA cables from the pre-amp outputs on the rear of the deck to the amp. I am having the same issue with the remote turn on wire.
you will have to "run" them from the back of the radio to the trunk, there is no way around it unless you use a "line output converter" http://www.sonicelectronix.com/viewcat.php?category_id=331&sort_order=price_asc for the RCAs and you can find a wire that is only "hot" when the car is on but i would just run them from the radio