AUX: You need probably 1v+ to get good level on aux input.
Headlamp sensor: The empeg has 2 dimming levels, one for lights on and one for lights off; both are settable, so it sounds like your unit is set for dim with lights off and bright with lights on! To set the level, go to the dimmer menu with the lights off, set the level requied. Turn lights on, go to dimmer menu again, set level required for this state. Done!
The empeg aux inputs have a floating ground, to adjust to your CD-head's ground level, so it should be ok. What do you mean "when he adds the CD head into the equation" - when AUX is selected on the empeg, or when the CD head is in the car at all?
Hugo