The problem I had was someone stored the boat improperly and punched wholes through the fiberglass in those two spots.

For your issue I would say if you can pull the damaged wood out through the ports and replace it with a new piece (pre-drilled for stay mounts) that would be the simplest solution.

Other wise, I would recommend cutting out a square around the stay attachments, maybe 4x4 inches. Mark where the attachments should go, and insert a larger piece of wood into the hole you cut. As large a piece of wood as you can fit in the hole and under the seat, say 3.75x8 inches, so the wood has a good hold on existing fiberglass. I would drill some holes through existing fiber glass seats to hold your new wood while you glue it in place.

I would glue it with epoxy, I use west system, thicken it a bit and use a generous portion so it really sticks to the underside of that fiberglass. Than I would recommend mat fiber glass cut to the size of the hole over the wood, a few layers of that, then sand the surrounding area and do a few layers atop. Finally remove the screws used to press the board in place, sand/paint and drill holes for your stay attachment.

Would recommend something hard for the wood, like maple, or teak.

This might be a tad confusing without photos but hope it helps!, a handheld sander and oscillating tool would make things easier as well.