So your EQ is what's being used to switch between the two inputs, right? And each of the inputs has two RCA cables, right? One from the Eclipse head unit and one from the empeg.

It sounds to me that if the Eclipse is pushing all six speakers in this config, then the empeg ought to be able to, as well, assuming that the EQ switch is (a) being used as intended, and (b) not broken.

Can you swap the units so that the empeg is input A and the Eclipse is input B? That way, we can see where the problem is by seeing which speakers are active for each of the components after the switch.