It sounds like the head unit's inputs are getting overdriven. I wouldn't worry too much about it, the head unit probably only wants 1v inputs. In that case, it's acceptable to reduce the empeg's volume to -10db or whatever it takes. If this is the situation, this isn't the installers' fault, it's just that the CD player wants 1v. Details Here.

Note: This assumes that your empeg is set to "flat". If you're overdriving the loudness or the EQ bands, then set that back to flat and see if the distortion is still there.

There is no provision to swap the channels in software, just swap the RCA plugs on the aux-in so it's correct.