I have a VW golf with a clarion head unit with built in amplifier and the empeg. I have the empeg installed on top it gets very hot if I go for a long drive (several hours). I haven't had any problems yet I wish I would have thought about that when I installed it and I would have put the empeg on the bottom. The Golf has a tiny compartment for the stereo also so there is not any air flow.

If you go with two head units I would put the empeg in the lower spot for sure.

I like having two head units with the empeg connected to the line in on the 2nd unit because if I go someplace where I don't want to / can't bring in the empeg (like when I go watch a band) I can just leave it at home and not have to drive in silence.