If you understand how to wire up a car stereo, it's really not that bad. Most of the time involved removing interior parts, running wires, soldering & taping connections, etc. Here's some info off the top of my head..
-The factory power feed (which consists of 3 small wires) isn't even good enough for the factory amp. In fact my connector was slightly melted. Definitely tape it off and run new wiring.
-Wal-Mart carries a decent Scosche amp wiring kit for $25 or so; it has everything you need (wire, fuse, grommet, terminals) to get power to the amp. I ran the power wire through the inside of the driver-side fender (there's a hole near the battery), and drilled a hole near the parking-brake cable to get through the firewall.
-The factory amp is mounted on a plastic tray in the top of the trunk. It's held up with a knob-shaped retainer on the driver-side of the tray that unscrews and pulls out, as well as two spring clips in the center. There's a hinge on the passenger side, so the whole tray swings down. The amp is held in place with plastic clips, which I had to snap off to accomodate the larger aftermarket amp. I used zip ties to keep it from shifting around inside the tray.
-You can get to everything easily by removing the rear seat and working from inside the car.
-The head unit's outputs are line-level, so I chopped off the factory connector and soldered on a set of RCA cables (which came with my amp wiring kit).
-As I mentioned before, the front & rear woofers are wired in parallel from the factory. I separated them by disconnecting the rears and running new wires to them.
-The factory amp has an internal crossover. As a side note, my biggest beef with the factory stereo was that there seemed to be a gap in the midrange between where the low-pass filter cut off and the high-pass picked up. For the aftermarket amp, I wired each channel's woofer & tweeter in parallel. I also put a 95uf capacitor in series with each tweeter to protect them from being blown out by low frequencies. The midrange response is much, much better now.
-I put an Alpine amp in my friend's car, which didn't respond to the HU's 6-volt turn-on signal. The antenna turn-on signal is 12 volts, but it cannot put out enough current to power both the antenna and amp relays. I managed to come up with a workaround, but to make a very long story short, get an amp that responds to the 6-volt signal.

My Sony amp handles it without any problems. I'm not usually a fan of their car stereo products, but I'm very satisfied with it and it certainly made the installation less painful.
I have the factory wiring diagrams on my computer somewhere; let me know if you need a copy and I'll try to dig 'em up. Good luck!