My power & remote turn on comes directly from my battery, so it runs through the engine bay, through the rubber grommet at the base of the windshield and then is routed under the driver's door rubber trim (there's a nice gap in there for the wires), around the B-Pillar, up under the side of the rear seat, and into the trunk where my amp is located up under the rear parcel shelf.
The RCA cables (need to be run away from power cables) are run from the HU along the passengers door rubber trim/B-Pillar, etc...