Re: pontoon deck
always a good idea' especially if you're going to lay carpet overtop. Seal the tops, bottoms and edges (most important) with a couple coats of epoxy. Use a roller for the faces and brush for the edges. Out of curiosity, what ply are you going to use? There are a few types of ply that are considered "marine grade"; but that mostly depends on how loosely the manufacturer / seller grades it.
Hope this helps!