How thick is the marine ply you're using for planking? Much beyond 3mm/ 1/8" I'd have to think a pneumatic stapler'd be the smart route. Remember to add thin, stiff plastic tabs under ALL the staples you'll be wanting to pull once things cure or you'll spend more time swearing at 'em that getting them to pull free. Plastic banding strap works well, the green, blue or frosty white (sometimes black too) stuff used in place of the blued steel strap they used to use for binding up construction materials.

If by 'bottom' you mean the LAST layer to go on, why would you want to leave 'em in? That's going to make fairing the planking nearly impossible.

If you mean the layer going onto the battens first I'd use Monel or plastic for their rust-proof nature. But why leave those in? They'll make pulling the hull off the battened forms tricky, or pulling temp frames & battens out once hull's complete.

First thing is experiment. Make small mock-ups of what you're proposing to do and give it a try. See how it works. I'm in the middle of a build and one of my golden rules is: "Don't do anything for the very first time ever on your boat." If you don't know it's going to work, don't do it. Do an experiment or two instead.

In my case, I've strip-built a deck for a 14.5-foot Sunfish clone. The strips were 1/4" thick Western Red Cedar, the forms were Cypress or Pine. The staples were to be removed. Nick Schade recommends 9/16" staples for his kayak builds so that's what I started with. Worked just fine with a hand stapler. Those staples don't go all the way down, so removal was easy. I used an upholstry staple remover (essentially a curved point with a handle) over a small scrap of wood to lever up the staples. Needed a pair of pliers for the occassional staple where only one end pulled up, leaving the other embedded. Went through an entire pack of 1,250 staples plus some and did not have a single failure where either the staple broke off in the boat or the staple went down far enough that I had to dig into the surface to get it out.

>> Use of a pnuematic or hand compression staple gun. <<

Hand will do just fine. And it's handy around the house, shop and boatyard. If you already have a pneumatic stapler it'll probably work as well but I wouldn't go out and buy one.

>> Type of staples, composite, monel, stainless steel, brass <<

Since I pulled all my staples out it didn't matter what they were made of. I used steel as that's most economical. Not sure what composite staples are. If you're going to leave staples in place they've gotta be monel, and probably shorter than I used so they'll be flush with the surface. Stainless fasteners have all kinds of interesting failure modes when embedded in wood with salt water. You don't want to go there. Brass staples would be a no-go. They're not very strong.

>> Leave metal staple in place for the bottom layer of plywood <<

It took me about an hour to remove all 1,250+ staples from my deck. I don't see why you'd leave them there in your build given that the weight of that many staples adds up, not to mention the extra cost for the monel staples.

Good luck with your build!