If the rot is extensive, the best plan is to pull up the entire cockpit deck. There are a number of core materials. We used Nidacore, it is light, & cannot develop rot. You still need to put thickened epoxy to seal the edges, and where screws go into the deck. Also a good time to check, and perhaps pull and clean--paint the fuel tank.
The new cockpit surface can be one of several materials; we used thickened gel coat, rolled out to give a pattern.