I would start by following Tony's advice. Bring another #12 black (ground) in from the battery, like you did for the +12v. You can in all likelyhood share the two #12's between your two headunits and just hook them up together right behind the units in the dash. Ensure that you have good connections throughout ie; if you are using lugs at the ends of your wire to the battery, solder them, etc. There are several other things to pursue, but let's start with the basics first. Keep us posted regarding your findings.

Tony: Do you know how much current is consumed by the Empeg on the switched ignition wire ? Or for that matter, all of its "sense" inputs ? I would think almost nothing, but I may be very wrong...