just thought i'd help give some more info on deadening...
I did my entire trunk (lid, sides, floor) with Damplifier. I also did my drivers and passenger door.
Damplifier is cheaper than Dynamat Extreme and has been proven to be the equivalent of Dynamat EXTREME. I ordered 80 square feet and it was perfect for my job. it is made by second skin audio.
You will need a small wall paper roller. the roller is like 2 inches wide or so. all you do is cut the pieces with a shop knife, peel the backing, stick it on and then roll it on well. you want it to last so make sure it is rolled down everywhere.
When doing your doors, make sure you do both the inner and outer walls of the door. i would start with the outer because you will need to put pieces through the holes in your door and it can get a little tight putting your hands in there.
Be careful when you are doing your trunk lid. Make sure you don't put any deadener past where the trunk lid meets the weather stripping. i made this mistake and when we got our first rain i had a puddle of water in the spare tire well. luckily my carpet wasn't back in so it only got on my deadener. It is a pain to remove the stuff so be sure you know where you want to put it and what areas you want to stay away from.
Overall, deadening is extremely easy, but it can be hard to twist your body in order to get it into tricky areas.
BHR you asked about covering the holes. I probably wouldn't put deadener over the holes, but one thing alot of people do is cut a piece of plexi glass and seal it over the hole. I haven't done this, but a ton of people on the car audio forum i'm on suggest it to really help the midbass.
hopefully that will be helpful!
the roller i used is sitting on the sill of the trunk.
not sure if i really clarified what the inner and outer walls are on the door panel. outer is closer to the outside of the car. as you can see i deadened there and it really helps.
try the knock test. knock on your door without deadener and then knock on a door with deadener. it is pretty cool.