Ok I looked at the service manual again last night, along with the head unit pulled. It is just like Jamikest said. Only source going to the factory amp is front left and front right.

From this source the amp sends the necessary signal to the tweeter and mid range in the doors and the lower frequency to the rear subs.

I pulled the pannel off on one of the subs, and turned the volume up on the deck. I put my hand on the cone and could feel it moving.

I spent over an hour adjusting crossover points, frequencies, eq settings and such. Finally I got it to sound good without distortion.

If someone wanted to isolate the subs in the rear, you would have to tap into the wire harness after the factory amp. Since the subs are Dual Voice Coil, you don't want to power them just off any deck. The lower impedance would probably fry it =) You would have to pretty much use an aftermarket amp that would support something under 4 ohms. Most head units only go down to 4ohms not less than.

I'll be working on some box ideas to house one of my 12" JL subs. I'm trying not to get too crazy as I don't want too much additional weight. Which is why I'm not throwing both in there Plus what little space I have, I would like to keep.