Hmm sounds exactly like what I just finished doing to mine. I added new door speakers which are 5x7/6x8 size, 2 amps, and an equilizer. The door panels come off by removing the 2 screws by the handle, and using the tool for the door clips, pops off from the bottom up, then lifting it out of the window channel, the speakers are held in place with three screws/bolts (1/4" drive I think) on the front doors, and 4 in the back door. I ran new wires all around, fishing the through the rubber accordians connected to the doors for the passenger doors, and outside of the swivel block on the drivers door, there is a notch that the wire can be fed through to the speaker. I mounted the equilizer in the center console, ran the RCA wires to the amps located on that cover behind the rear seats that folds down when you fold the rear seat down. Ran power from the battery to the amps on the drivers side. Connected the speakers to the amps, and since I have the rear radio controls, I found the wires for the rear speakers and spliced a line converter in place to plug in the equilizer. The radio does everything except for the fader now which is controlled by the equilizer. I have a Coustic equilizer with front, rear, and subwoofer controls along with 7 bands of equilization, an amp for the door speakers, and an amp for my MTX subs.
If you want I can take some pics to give you an idea, although I haven't had time to finish dressing the wires and cables yet.