The rear 6x9s are really are two different speakers the way that they are set up. I think it was done that way to keep the same stamping.
If want to, you can splice the wires going to the bass part of the 6x9s and drive your own sub. I tried it with an MTX 12" and it was fine, but a little boomy because of the crossover and boost in the amp. You can't drive a full range speaker with that output. You will only hear the bass.
I didn't like the way the 2" fullrange sounded. I tried connecting the fullrange channel to a regular 6x9, but there was way too much treble from the treble boost and it sounded like crap. It could have just been that the 6x9 had two tweeter sized speakers.
I ended up leaving my upgraded 6x9s in the stock location and just driving them with the bass channel from the amp. I cut two holes in the rear deck and mounted 4x6s that I had from my old car and I tied them to the fullrange channel. They sounded really good. I then added a sub by tapping the rear channel lineouts going to the amp, so I wouldn't have that crappy bass boost. Since the 6x9s handled a lot of bass, I set the crossover on the sub at 45Hz. I also replaced the factory speakers up front, and I think it sounds great with the stock head unit.
