You will be much better off with a proper amplifier and wires run to the trunk. Burying an amp in the dash is actually more trouble than mounting one in the trunk.

Take the time, and do it right. There's a lot more satisfaction in having a good system than a half-assed one.

Regarding the tuner: It only activates when it's in the car. If you want to make the docking sled think it's in the car, you must supply it power via the car wiring connectors, not through the home power jack.