Brandon I have to think that the muffled sound is coming from the fact that they don't have the ability to move any air when stuffed under a seat. Many people have cut out vent holes in the seat bases to let subs breath.
Your setup should really rock, you've got some high quality components you're using.
Can you post any pictures of the setup? How are the subs orientated under the seats, are they firing up/down/side, etc..
How far is the cone area away from the seatbase?