I know that can add noise, but will it add engine whine?

Most definitely.

Noise == Engine Whine == Pops/Clicks == Etc.

All of these things can be caused either by ground loops or by inductive noise. Did you get those PDF documents? Did they help?

Also, how do I filter the power leads and is it even recommended (will a filter degrade the signal?)

I use the heaviest-duty power line noise filter that Radio Shack sells (20 amps). It's on the power line that feeds my amplifiers directly from the battery. Before installing the filter, I put a 20-amp fuse on that line and cranked the amps and tested it for a while to make sure the amps wouldn't draw too much current. I still have the 20-amp fuse in place, too.

I also have the Empeg itself feeding off of that same filtered power line.

If you have more than one amplifier, or particularly beefy amplifiers, you might need to find a bigger filter or use a separate one for each amp.

A power-line noise filter will not degrade the signal, since it doesn't filter the signal cables (it filters spikes out of the power line).

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Tony Fabris