Naio,
If you can get to the surface on the other side, and can put a piece of tape there to block the patch material, I would simply fill the holes with epoxy, if your dealing with a vertical surface then I would let it start to solidify slightly (just till it starts getting thick) and fill to about 1/8" above level, let dry for a day, and then sand lightly to smoothe the surface and then paint to cover.
OR,,,
If these are just some small 1/4" holes for mounting bolts, again if it is only the single thickness of fiberglass, you could place another bolt through the hole and a nut inside to secure it. Put a rubber washer both outside and inside to create a seal. And you should be done.