First off, a dual sub box is way to big for the back and there is going to be way too much bass for the back hatch to handle I have 1 12" Sub in a 12" 1.75 cubic foot slot vented box and even that is way too much for the back. Even in my Explorer the sub would rattle everything on the outside of the back hatch. Inside it sounded wicked. It would make your hair stand on end. But to get the stock stereo out it depends on when year Cherokee you have. If you have an model then the whole black dash covering has to be taken off(4 philips head screws) then the stock headunit should be held in with just 2 philips head screws that you unscrew and the unit should just pull out and you disconnect everything from the back of it. If you have 96-01 then the only thing you should have to pull off is the covering over the stereo, and heater control knobs. As for the amp, you should not mount it underneathe the rear seats. Amps create heat and they should be out in the open for the proper circulation to cool them(air cooled). Ive had mine so hot you could not touch it w/o getting burned. Just mount the amp in top of the box and run the wiring to it so if you need to take the box out you can just unscrew the wires to the amp and everything will come out. Simple. As for getting a headunit and speakers and the amp, box, and sub combo, you should go to
www.crutchfield.com where they have great deals, free shipping, DETAILED instructions, free mounting brackets, and free wiring harnesses for the speakers and headunit. Have fun!!!