Refer to the pics below and use them as a guide to rewire your head unit to the amp power lugs. These are a few examples of common stereo installs, and there are a couple of iterations of stereo power switching.
Wiring the head unit to the amp as shown has proved to be the best way to prevent noise in an audio system.
What is your charge voltage when the motor is running? If you have ever switched your Perko switch to OFF or past OFF with the motor running, you could have blown a voltage regulator diode. That can make nasty noise, and will cause other problems as well.