I run a Jensen four-channel amp for my fronts and rears, and I also have a single bridged subwoofer running off of another Jensen amp. So I've essentially got the same amplification setup that you do (albeit with more power and done with two amps instead of one).

At first I opted to do it this way:

Empeg Fronts->4ch Amp Fronts
Empeg Rears->4ch Amp Rears
4ch Amp Rear Pass Through->Subwoofer

This meant that I could control the front/rear fading from the empeg, and the subwoofer level would simply be part of the rear speaker level.

This worked, but I realized that I was never adjusting the fader at all, I always left it in the center. I had a certain setting where I preferred the front/rear ratio that was kind of critical to get the soundstaging the way I wanted it. I had that front/rear setting dialed in pretty well using the amp's gain controls and was satisfied.

On the other hand, I did want to adjust the subwoofer separately from the rest of the speakers, and I couldn't do it with that setup. Subwoofer adjustments meant opening the trunk.

So I re-wired it to this scheme:

Empeg Fronts->4ch Amp Fronts
4ch Amp Front Pass Through->4ch Amp Rears
Empeg Rears->Subwoofer

This means I can't control the front-rear fading, but the fader is now my subwoofer level control. Also, miraculously, this new routing scheme helped cure a ground loop problem I was having, although that's totally unrelated to the discussion here.

Either one of those two methods is valid for you. Note that if your amp doesn't have pass-through plugs, a simple pair of Y-adapters will do the trick. You could also simply "daisy-chain" a single pair of outputs from the empeg into all sets of amplifier inputs, and the fader will do absolutely nothing. This is fine, too, if you're willing to set all of your relative speakers levels with the amp gain controls.