Center console is fine for the RCA's
The only thing to watch out for is the car's main power wire when running speaker wires (they run down the passenger side of the car). So, it's best to run the speaker wires down the driver's side. Since you're using the existing speaker wires, you don't need to worry about this.
There are two rubber grommets in the rear deck - one on each side of the car. The passenger side has the car's main power wires running through it. I would route any additional wiring through the driver's side grommet (to keep them away from the vehicle's power wires).
I believe there is a capacitor used as a filter in the door panel. I would bypass this if you're using the Alpine mid and tweeter combo with the Alpine crossover mounted in the trunk next to the amp.