I'd suggest getting a 4ch amp, some components for up front, and a single 10" or 12" in the trunk. It definately sounds like you're on the right track.
Use the front channels of the 4ch amp to power the components, and bridge the amp's rear channels to the sub. Just run your rear speakers off of your HU. It's a fairly simple setup, and the install is not difficult. You could probably stay below $500-600 and still have some quality equipment. Post your budget if you'd like some specific suggestions and where to get them.
