Travis - no question is silly on this site - that's what's so great about it!
I just realized you don't have any benches do you? Only the 2x4 or 2x6 that stretch across... If that's the case, here's how I would deck it if it were mine.
In the bow of the boat where it starts to level into the floor - this is where I would make my deck, and if there are no benches, then run it all the way to the rear stopping shy of the transom by about 12"... this will give you room for your battery and a few other things like anchors and such.
I would take the 2x2 and run them perpendicular to the length of your boat, with 1 2x2 spaced every 18". This will give you about 8' to work with for decking (start 1 foot from front of boat, then stop 1 foot short of the transom). That will be about 6 actual 2x2 braces placed 16" on center. I would measure each board and cut them one at a time because I doubt each will be the same length - remember, you want them wedged in there since you don't have anything to attach them to.
After getting a dry cut fit for them, measure for your 2x2 braces which will run in between each of your cross braces you just dry cut. I would put them about 2" from the gunwhales on each side, and 1 on each side of the center line of the boat about 12" apart. I wouldn't put any benches higher than that on a 10' boat because it can be unstable, and the last thing you want to do is flip over in the water when you rare back on a big hawg!
Once you have all of your framing done, I would use 1/2" ply because of the size of the boat and the amount of bracing - this will be plenty of support for you.
Seats... I would use 12" pedestal seats like you can get at walmart (black with 3" diameter pedestal). I would use bolts and nuts to mount those to the deck. But since you are using 1/2" ply, make sure you cut another piece of ply about 12" long by 8" wide to fit between the center braces and put that under the main floor. That will be 1" of "beef" for your pedestal to mount to. Same goes for the rear seat.
As far as adding storage... you can cut out sections between the frames of your floor and use piano hinges so you can open and close them. I don't know what the bottom width is of your floor, so it's hard to tell you the dimensions for that out of my head, but honestly, it's probably not going to be that much room becaue you'll probably only have about 4-5" underneath the deck. One thing you can do is make you a center bench (not to put seats on) and use that for storage. Just make sure that when you put the hinges on it you do it so that the lids open from the rear... you don't want to be going down the road and the wind blow up your lids!
Battery in the rear... you can build another bench at the transom for storage of your battery and other things like life jackets, anchors, etc.. Just make sure you leave a section in the middle open for where your trolling motor will attach.
You asked about water and such... it would be best to use some type of water sealant or deck paint to paint all of your wood.. this will help deter wood rot and moisture build up and will let your decking last a while longer. Be sure to use NON PRESSURE TREATED ply when you do this. You want to use exterior plywood because pressure treated has copper and it doesn't mix with aluminum very well.
Once you get the wood off/out of your boat, take more pictures, because everything I wrote could be changed up quite a bit depending on a few things... but hopefully this will give you an idea of which way you need to be heading.