Re: quick question on floor replacements...
Your boat floor, if it is wider than 4 feet is built in sections of plywood running across the width of the boat. Those sections are joined together, generally, over stringers or frames that are constructed under the floor.
Wherever two pieces of plywood come together, there needs to be lumber underneath to screw into. A boat's floor is part of its structural strength and the flooring is mechanically fastened to the stringers & frames with stainless screws and adhesives. Then the edges of the floor are glued, puttied, or epoxied to the insides of the hull where they meet.
Once the floor is mechanically attached to everything, then you cover the entire floor, and up the sides and transom, with fiberglass to protect the wood from water and also to add more strength by tying it all together again.
The spots you have found are not going to be the only rot you find. There is probably allot more lurking that will show up when you start removing things.