What year is your trailer? I have an 08 which uses a welded aluminum frame roof with a thin sheet of plywood on top. The aluminum is welded with lateral and longitudinal pieces to form a grid. My roof has TPO roof material, similar to a rubber roof. You would want to peel back the TPO then cut out the damaged plywood and replace. The TPO is just secured on the edges with sealant and floats on the surface of the plywood. You want to cut the plywood so the edges are supported by the aluminum frame. Set your saw blade slightly less than the thickness of the plywood, cut and gently pry up with a chisel. I would use a marine grade plywood and varnish it. Use countersunk self tapping screws to attach the wood to the frame. Just remember not to go too deep, otherwise the screws will poke through the ceiling. Also make sure the screw heads do not protrude above the surface, otherwise they will wear holes in the TPO. You will then need to re-seal the roof with a sealant compatible with your roof material. If you don't know what you have, call Funfinder and they will tell you, I call them every now and then and they have always been responsive. You may need to patch in a new section of TPO if it tears. I have not done this before, but you should be able to just cut a piece and glue it down with the correct sealant.
If you don't want to cut out the rotted section, I have used a product called GIT-ROT which is a very runny two part epoxy. This will soak into the wood and dry creating a very hard surface. Finfinder uses a varnish on their plywood so you would first want to sand that off so it can actually soak into the plywood. You would still need to remove the roof material and re-seal afterwards.
Just remember, if you start a repair and then decide you want a dealer to finish it, they may charge more to fix a botched job. On the other hand the best way to learn something is to jump in and try it yourself. Good luck.
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