h: sorry, i could have sworn that I read your post word by word so this wouldn't happen (me looking like an idiot).
Anyways, if you're planning on installing an amp now, you can just run the wires along the side of the car, right behind the panels (that way you don't have to remove the carpet like you were wondering). Its generally a good idea to run power wires on one side, and the signal cables on the other side to avoid picking up unwanted sound. Its very simple to hide them, I would just suggest that you take your time when you do it.
I'm guessing you have an eg, otherwise I would have posted pics oh how I did mine. I think all the later civic 4 doors have 6x9's in the back. Have you decided on a set of speakers yet? Also, the best thing to do for brackets is make your own using 3/4" MDF because the plastic is more likely to vibrate and its annoying as hell - at least it is to me, but i'm anal about sq.