Yep, I did leave the carpeting in place. I just trimmed out all of the cardboard backing to make it as acoustically transpearant as possible.
I also used some 3/4" felt carpet padding between the metal of the rear deck and the rear deck cover. It made a world of difference, completely eliminated all of the rattles.
I'm planning on putting another 8" sub in the rear deck on the other side in the same configuration for a little more bass.
Just not enough time and too many different projects going on right now.
In any case, cutting/drilling holes in the rear deck is unnecessary. Just use some 3/4" MDF to bottom mount the speaker, trim out the rear deck cover, and use some rattle-preventing insulation. It'll definately fill the goals you're describing.
