During some research while rebuilding my transom, this is what I learned about plywood. Marine plywood does not resist rotting any better that regular cdx type ply. They both are made with the same type glues. The major difference between the two is that the marine ply has no voids in its core. You know those football shape patches you see in regular ply. Those are only on the outer layers of cdx ply but are used to fill knot holes and such throughout the layers of marine ply. Thus the marine ply is somewhat stiffer and stronger. I would probably guess that the ply in the floor of your boat is not marine grade ply, but is regular cdx. What ever grade ply you deside to use make sure it is seal properly(both sides). I use a product called Rot Doctor CPES for a sealant on all of the new wood in my boat. Other may suggest using fiberglass resin thinned with alchohols and like materials which is a cheaper route. That is up to you but check out the Rot Doctor web site and deside. All of the wood then need to be coated with a regular layer of resin to completly seal it . As far as what thickness do you need, if there is a floor drain you could remove and check thickness or you could cut out a small piece and check. Be carefull cutting out the floor as there are probably stringers and other support members under there. Good luck with you project !