Your sig says you have a master angler but the boat in the pic's is a 20sf. Was your fuel tank above or below the deck? There is a reason I'm asking. You asked about pouring foam under the thin glass skin that you have now. If your fuel tank is under the deck then make sure you dont pour foam in that area or it may raise the tank. If you decide to pour foam make sure you drill lots of 2 inch holes for the foam to expand upward so it does not buckle the skin upward.
Now that I've said all that I'm going to tell you that the best way to fix your rotten deck is to completely remove everything exposing the stringers. Leave a 2 inch lip of your existing deck around the perimeter for the new deck to sit on top of. You will have to raise the stringers slightly as well. Go to Hermco's web site and see how he did his boat.
Here is a pic of what my boat looked like under the removed deck. The foam was sparse and randomly poured. Good luck.
strick