Seat tops don't flex as much as the hull, so lots of stuff will patch the holes. JB Weld or 5200 would be fine. That green stuff that Cabelas sells to patch hulls is another option. Even that black gasket maker stuff will work there. If you want a nicer finish, I'd try some type of epoxy thickened with powdered aluminum. Make sure the foam in the seat is dry before you seal it up.
I'd install some type of round inspection port in the back of the bench if it serves as a flotation chamber, although you'd probably have to chip out foam to see the bottom. I hate sealing anything on a boat without a way to get back in there, even flotation chambers. It is my pet peeve and is based on my experience that all boats will leak eventually. Many guys seal foam up forever and do fine for the life of the boat.
Nate
