I set up a (cheap) amp, subs and head unit in my civic YEARS ago. hardest part was pulling up the carpeting to run the wires cleanly. I gave up once I did the front, and just ran them over the seats in the back since I rarely had someone sitting in the back seats.

If you have a switched 12v lead in the trunk (for the amp), plus L & R audio wires then the install in the trunk is pretty simple with some tools. Some dampening in the trunk lid helps with rattles, if you get any.