In my car I cut out the factory box to fit a 10 inch infinity kappa sub and I have a jbl amp that is under the passenge seat. When I bought the car the wiring was already run (there was a crappy amp there and a crappy sub in the stock box) I don't know how hard the wiring would be because I didnt do it, but the wires come from the head unit and go under the carpet on the passenger side and then come up through holes in the carpet under the passenger seat (the holes are there from the factory). From the amp I don't really know where they ran the wires, but they go back under the carpet and behind panels I presume to the sub. It seems like the hardest part about running the wires would be removing and re-installing whatever you need to to run the wires. And as far as hooking everything up I'm sure you could find any info you need on here, people are friendly, knowledgable, and willing to help.
this is the amp, just so you can see where it is
http://i183.photobucket.com/albums/x...9/100_4137.jpg
and what I did to mount the sub(I had to get a thick piece of wood and screw it on because the box wasn't deep enough for the sub)
http://i183.photobucket.com/albums/x...9/100_4139.jpg
hope it helped...