Sorry, I just hear Best Buy this and Circuit City that all the time...and if I explain politely that putting a $30K car in the hands of those morons is a bad idea...people don't get it.
First off, are you just installing a sub or are you going to run full range speakers off your aftermarket amp?
If you are just connecting a sub, you can simply use the audio signal that goes into the stock rear subwoofer. The sub harness has power, ground, and audio +/-. I didn't go this approach so I can't tell you what color wires are for the sub. I know the info is out there though.
If you are connect an amp to run full range stereo speakers, first remove the passenger seat. That will give you easy access to the amp. Next remove the metal plate that the amp is attached to. The amp is mounted upside down on the back of this. Disconnect the wiring harness. Using the wiring diagram in the sticky thread find the left +/- and right +/- wires and strip about 1/2" of the sheath from them. Take a cheap RCA extension cord (with female ends) and cut one end off so you have about 6-12" to work with. Prep the ends so you can solder them to the appropriate wires on the harness. The center wire is + (positive) and the outer wire is - (negative). Double check these connections with a multimeter (available at Radio Shack for $20-30...and worth every penny). Now you can just hook up your RCA cable and run it to your amp. Also in the harness should be a remote-turn-one lead. A wire that only has +12v when the car is on. You can use this for the remote-turn-on connection on your amp.