I just installed a new stereo (although Exile ZLD) and am having the same issue. Mine is a constant whine if you will. It is only present when the engine is running. If the motor is off, no whine exists.
With motor running, the whine is present in all in boat speakers and the tower (2 different amps).
When music is playing you can not notice the whine, however when the volume is turned down or the song ends and there is a couple seconds pause before the next song starts it is quite noticeable.
All 3 of my amplifiers and Exile ZLD share the same ground point. The amplifiers have a common power source. The ZLD gets power from an unused accessory switch on the dash from the factory. The head unit power&ground is from the factory harness.
My next change is to switch the HU to ground to the common amplifier ground point, and change the HU ignition wire to the same switch as the ZLD and amplifier remote turn on leads. (will make it so my stereo doesn't cut out when turing the ignition key)
Is the location of power source important? or is it mainly just having a common ground?