First off, if you havent bought the amp yet, look for one with high level inputs.
http://www.crutchfield.com/S-9LSX8q2eq6R/cgi-bin/prodgroup.asp?g=120&avf=N&nvpair=AG%5FNumber%5Fof% 5FChannels|FF4%40Channel&nvpair=AG%5FGeneral%5FFea tures%7CYCSpeaker%5FLevel%5FInputs#see_all
that is a link to the crutchfield site. All the amps listed are 4 channel with speaker level inputs.
for the wiring, what I would do is pull the HU out of the dash, and pull all the stock speaker wires. At the speaker ends, unplug the wires, and tape on the new ones, that way when you pull, the new ones are already run. This will probably require some finness, and probably some time. Then, run the stock wires to the speaker level inputs on the amp, and viola, all ran. I would mount the amp under the driver or passenger seat, or under the back seat if you have enough wires. I hope this made sense, if not, ask.
1999 XJ 2WD sport I6, AW4, 8.25, Black
RE 2" BB, 30" A/Ts, intake, exhaust
custom built rear storage box with drawer and sub.
1988 XJ Cheif, 4.0, NP231, D30/D35.
4.5'', 33s, 4.56, lockrite, recovery points, skids
K&N cone, flowmaster, cheap speakers, and LOTS of dents.
Plus a pretty black bike