What head unit are you using, a stock one?

The monsoon has a real funny ground/signal system to turn the amp off and on. I can't remember the specifics offhand. I do know that it sounds like a real PIA to hook up, and the amps go bad after a while anyways.

If you don't like the sound coming from an aftermarket HU, adding an aftermarket amp would be much easier. I'd take the monsoon amp out of the car, personally.