The winter of 1999 - 2000 I totally overhauled the interior of a Lund American 5.3. If your boat was anything like that one, the floorboard screws are under the carpet. In my case the carpet wasn't worth anything so it was coming out anyway.
As previously mentioned, there are a lot of screws. So what we did when we reinstalled the new floorboards, we first basically made a map of the "floor" of the boat. We mapped out where all the previous screw holes were. The reason we did that is because we wanted the new screws to go into fresh metal to ensure a good bite.
I was a fun project, it enabled me to improve upon some of the compartments and things like that. That being said, I'll never do it again.