I did something similar to that red car with 2 12inch type R's and 6X9's on either side as well.
Here are a couple pics of what i did.

I cut a new piece for under the box as well out of 3/8 OSB to give a little more support than the stock trunk floor.
The center boxes are 5/8 inch MDF top and bottom with 3/4 inch MDF sides and center divider.
The 6X9 boxes are 1/2 inch MDF.

The black piece is 1/4 inch plywood covered in vinyl. It is held down by the 6X9 covers.
The white piece is also 1/4 inch plywood covered in vinyl that just tucks under the weatherstripping all the way around the hatch. That way the white pice can be taken out in easily to get to a very limited amount of storage beside the boxes.
My amps are mounted behind my back seat just to keep them out of site.
hope this helps.