welcome aboard!
You're right about pressure treated - the copper that is in it does not mix well with aluminum.. Use exterior plywood instead.
The thickness really depends on what size boat you have, the type of framing that you are going to use to support it, and how much weight it's going to have to support.
For raised decks, like in the front, If you have sturdy enough bracking you can get by with 1/2" ply. I think I used something just a little bigger than 1/2", but I can't for the life of me remember what size it is. It would also be a good idea to add an extra piece of ply that is about 12"x12" under where your seat will be. For floors that are raised off the bottom of the boat just a few inches, you can make a subframe across the ribs, and lay a sheet of 1/2" over that as well.
As far as benches, if you plan on putting pedestals in them, it would probably be a good idea to use 3/4" ply and attach it to the bench with either Stainless Steel lag screws (3/8" x 3").
Best sealant you can use on the transom is 3M 5200... it comes in a tube and you can most likely get it at Wal Mart, but that is some goooood stuff!
Post some pics of your boat, and we can help you out a lot more.. hard to do it off imagination when we don't know what you have.
edit* Joe beat me to the punch! :beer: