I'm not sure what scope of help the OP is looking for, but here's a quick rundown...
More or less you have to get power and audio to the amp (usually) in the trunk.
Power: most people use heavy gauge wire (4 or maybe 8) from the battery (with a fuse) to the trunk. Then use the same size wire to ground the amp. Where you run the wire probably depends on whether you want to see it or not.
Audio: There is 2 ways to do this (that I know of, I'm certainly not an expert).
One is to use "line level" or speaker inputs on an amp. For this you pretty much splice wires into the rear speaker wires and hook them up to the amp. The amp takes that signal and amplifies it. I've never done it this way, but it seems like it would be the easiest. The audio quality suffers though.
The other way is to hook up RCA cables between the head unit and the amp. Buy some long, high quality stereo RCA cables and run them between the trunk/amp and the dashboard. You'll have to snake them through the dash, which is a pain, to the back of the deck. The problem is: I don't think factory head units have RCA outputs, so you'll need to buy a new deck if you're going to go this route. Oh, you'll also need to have an "amp turn on wire" which is a small wire that connects the deck to the amp to remotely turn the amp on when the stereo is on (so it doesn't drain your battery while the engine/stereo is off).
The advantages you get with RCAs is you get a better signal and also sometimes a customized signal. Some decks have a sub-output that only puts out the low frequencies suitable for subwoofers. This will let you control the relative volume from the deck instead of having to go to the trunk to make adjustments. (Got your parents in the back seat? Turn the subs off.)
Oh yeah, if you do get a new deck you have to hook it into the car's wiring. To do this you'll need a "wiring harness" that is compatible with your vehicle. A wiring harness is basically a plug or a set of plugs with a ton of wires coming out of it. You connect those wires to the wiring harness that came with the deck (don't worry, they're color coded for the most part).
Long story short, it's really not very hard, but if you haven't done it before it can be a time consuming challenge. If you can get someone that has done it at least once before it would help a lot!
Crutchfield is expensive (I think they may have gotten better in the last few years), but they have what you need and will let you know all the pieces you need before you complete your order. They also have the tools that are required to get the factory stereo out in the first place. And I think they send you instructions with diagrams/pictures to help with the install. In the end, the extra expense may be worth it for a first-timer.
