Sound System Setup

I just bought a new 96' Cherokee 4dr 4x4 sport, and I want to put my stereo system in it. I have a pair of 5 1/4" 2-way pioneers, I have a pair of 6x9" 3-way pioneers in boxes, and I have a 12" Rockford Fosgate and amp in a box, and then a pioneer head unit with three preamp outputs. So My question is what would be the best way to hook all that stuff without replacing the stock speakers? I don't really have the time to replace everything, and I don't want to pay for it to be done. I've thought about running a new tri-mode amp to the 6x9's and the sub, but I'm not sure what the best would be. Should I take the time to put the 5 1/4's in the front doors, and then rig something up in the back with all the other stuff. Is it terribly hard to install the speakers in the front doors or in the roof rack in the back? Also, my sub and box are pretty big, do you guys have any other space saving alternatives with different subs that are cheap (I'm a poor college kid). So that is what I've got, and I'm just trying to figure out the easiest way to get the best sound while saving space time and money.