Take out the rear 6x9's. You won't need them after you have a nicely setup front component system. Also by having those speakers back there the subs are going to cause them to distort and sound even more crappier. Also when you take out those rear speakers you are allowing more bass to get into the cabin.
For deadening the rear deck you will want to use a bunch of pieces of mat, not just one big sheet. That will cause wrinkles and you won't really be doing a good job of effectively deadening. Instead use 2-3 layers of smaller peices.
The way I would deaden the rear deck is about 2 layers on the top of the deck, then one lyer on the bottom. Then use some foam inbetween the deck and the deck panel. This will halp diffuse any rattles between the rear deck and the deckpanel.
www.sounddeadenershowdown.com See which deadener is best for your budget.
I chose and reccomend
www.raamaudio.com He also has Ensolite foam which is good stuff for between the deck, and the decklid.