Another possibility is the routing (and quality) of your RCA cables. They can pick up the noises you described along the path between the Empeg output and your amp inputs.

One experiment you can try is to temporarily bypass your current RCA cables with a new pair that stays way clear of any other car wiring. If this eliminates the whine and switching noises, it's almost surely a coupling problem with your current RCA cable routing. If this is the case, rerouting away from other wiring and using higher quality (stronger shielding) cables should fix this problem.

Good luck