The sides of our coach roof (cabin top) are 35 year old plywood with 35 year old fiberglass above it. The portlights started to leak over the winter, and probably had a bit of a leak before that but this winter was one of the wettest San Diego has seen in a long time.
I've yanked them all off, and sure enough there's a significant amount of delaminated and rotten plywood lurking behind the fiberglass. Fiberglassed over wood seems prone to this type of behavior. The relatively tough fiberglass skin doesn't crack or swell until significant damage has been happening for a long period of time. With simple painted wood, the paint will crack quickly and the damage much more localized.
For this type of work I just let it dry out in the sun, get a lot of liquid epoxy in, and then start building up with epoxy combined with fairing filler. Get it to finger smooth, a final coat of liquid epoxy, 220 sand it, prime it, and paint it!
Over on thekeel.com, Mac added some valuable tips on just how nasty a cabintop leak can be.
I'll post another picture when it's completed, but I thought an image of a halfway finished product might be helpful for some folks. Also, I'd recommend using a sanding block instead of power tools for the final fairing. The hand block (which has a comfy rubber grip) will do a good job of an even sanding. After as much work as it takes to repair something like this, it's worth taking a few more hours to get the sanding right.
And remember to put a final coat of liquid epoxy over the lighter fairing. The lighter fairing compound isn't as strong to dents, will make the final product smoother and more water resistant.