You talking the wood floor right? I just did mine this year although I have not had time to paint it yet as the weather, rain , kept me from finishing it and the fish came in so I put the crappy old floor back in until I get a chance to paint it. BTW Eddie today would have been a very , very, good day to be layed off.

Alright back to the floor. I just used regular exterior plywood. I am too cheap for marine grade, which would be better. I sealed the edges with epoxy and I am going to use an exterior porch paint recommended by Steve, Capesams. Here is the product.
http://www.californiapaints.com/PorchNFloors.html
Epoxy fortified and no primer. I would not recommend any type of carpet as it will get wet and stay wet and stink with fish slime, blood, etc... I use stainless screws and they go into the ribs of the boat and the pressure treated support board running the length of the boat that supports the center of the floor, making sure you choose screws that are not too long

. Just lay the pieces you take out and trace and cut. Pretty simple. Should last several years. In a perfect world I would encase the whole floor in fiberglass but I am too lazy. Hope that helps.