I have a houseboat and as you can imagine moisture and plywood rot is always on my mind. The boat I bought had already lost some plywood.
What I have found is that the new plywood itself needs to be protected from rot first - primer. Then a coating put over it.
Fiberglass over plywood by itself has a tendency to allow moisture to get between the glass and the wood, then rot. A product called CPES is the best I've found. (one of those an ounce of prevention things.)
What is CPES Primer?
Clear Penetrating Epoxy Sealer (CPES) consists of a tough, flexible resin system in a solvent blend which aids in the restoration of rotted or deteriorated wood and the protection of new wood. The Epoxy Resin system chemically adheres to the wood fibers and significantly strengthens them while allowing for normal expansion and contraction.CPES is effective because of the special blend of solvents that allow it to migrate into the wood fibers and into the cellulose of the wood. Impregnation of the wood with the Clear Penetrating Epoxy Sealer changes the cellulose of the wood (which the bacteria and fungi find easily digestible) into epoxy impregnated cellulose which resists the fungi, while reinforcing the wood, and accomplishing restoration.
CPES is a two-part product. Mixes 1:1 equal parts of A and B by volume. Apply with brush, roller or immersion. Will cure down to 50 F. Also called MultiWoodPrime, CPES makes an excellent
paint and varnish primer as it chemically bonds the finish deep inside the wood grain.
More info...
http://www.epoxywoodrestoration.ca/price7_050.htm
Here are some tests showing the benefits:
http://www.rotdoctor.com/test/polytest/polytest.html
One place to buy
http://www.star-distributing.com/smith/cpeswhy.html
I hope this helps.