[YourConfused]

I'm not sure if this will help or not, but here goes.

I used a combination of 3M adhesive backed neoprene foam, spray on dampening stuff and Deadbeat (dynomat stuff) on my car. I used layers of fiberglass in the trunk to reinforce the floor as well.
The doors, back deck and insides of the sub enclosure got the foam, while the inside of the sub enclosure got the deadbeat under the foam. I think I put deadbeat on the rest of the trunk floor too. With the trunk lid being fiberglass I didn't wory about it resonating and just left it alone. The insides of the doors got the spray on stuff.

After all this I don't hear any rattles due to the volume of the music. There was no before and after for me. I have noticed that putting dynamat or whatever on the back of the license plate almost always eliminates allot of the rattle noise from the trunk area. If your system is rather powerful I would also recommend using lock-tite on bolts for the hinges and latches as I have had them rattle loose.
Hope this helped in some way.

p.s. I am not sure what you are referring to as the upper and side carpeting.