I'm going to mount my amp upside down in the trunk. I've done it with an alpine 4x40, and it fit perfectly in the square dip under the 3rd brake light.
Now I have a JL 300/4v2, I will mount it to a cutom fit mdf board, 3/4 inch, that hopefully will span the entire underside of the rear deck. (photos soon)
Eventually I want to add a thin mount sub (JL 12TW5 or 13TW5), centered under the rear deck, facing down. It requires a 4 inch mounting depth, made out of 3/4 mdf. Probably make it 6 inches total (4.5 mounting + 1.5 inches of mdf (2x3/4)). Amps on both sides, 500/1v2 for the sub, both facing down, along with a capacitor.
I just want to keep the components out of the way, and retain my trunk space.