I got a whole setup from Crutchfield, and installed it on Friday night.
Take the harness that connects to the 2 "outputs" of the amp. The 3rd plug (the one on the furthest right side of the amp) is the input from the factory HU.
Take the harness you've got, and add about 18" of wire to each, then splice it into your new aftermarket harness that comes with your stereo. Colors should match up. Don't connect the power antenna cable to anything.
This bypasses the factory amp, but uses the outputs from the amp to the 4 door speakers. I lost the miniature dash speakers, which were crap anyway.
The plug-ins that are right behind the factory HU just don't get used.
FYI, Crutchfield's information showed every step and had much more detail than I expected. The only thing they should have said instead of just extending the wires was how long to extend them, or make their connecting harness have about 2ft of wire on each, and then you can shorten it to match your setup.