the floor is rotten because the underlying structure is rotten. start by removing the old floor, then remove the rotten structure, and keep removing rotten material until you get to good material.
on a 52 year old houseboat with a fiberglass hull and wood stringers and transom, you may have to go all the way to the hull, and replace transom and stringers.
putting a new floor over a rotten floor is neglecting the structure and will lead to your new floor failing in a very short period of time. its called a "deck-over" and is the boating equivalent of a used-car dealer using the sunday paper and 5# of bondo to cover rust holes. may look pretty for a week until you get it home, however will fail in short order.