My HU now is an Eclipse (not the car, the car audio), so it's not factory.

Ah, I see. I assumed that since you were talking about a Mitsubishi car, and said the stereo was an Eclipse... well, you see where I had been confused.

It sounds like no matter what, I can ditch the additional eq.

Not if you want to leave the empeg at home. You said you work in the ghetto, so if you can't bring the empeg into work with you, I would understand the need to leave the empeg at home and would agree with doing it that way.

I think our lack of understanding about the problem stems from not knowing what the input/outputs of that external equalizer are, and therefore not understanding how it's hooked to the amp and why pressing its button causes two of the speakers to stop working. It would be nice if we could get more details on that.

You said the head unit has three pairs of RCA preamp outputs. Are all three pairs connected to the equalizer? You've also said you have a 4/3/2 amp. I assume that means it's a four-channel amp with the capability of either pair of outputs to be bridged mono (for a 2+sub configuration or a more powerful 2-channel configuration). So if it's a four-channel amp, how are six speakers getting driven off of it? What is the wiring scheme actually like?

Before we can answer your connection questions, we really need to know how things are hooked up right now and what the possible hookups to the equalizer are.