Any fiberglass areas that are loose, delaminated, bubbled, cracked or which show staining from water intrusion should be removed (cut away, heated and peeled, sanded or whatever it takes) back to the point where you get to securely attached, undamaged fiberglass. Then you feather out the edge of the good glass around the hole for a couple of inches and sand the surface of the exposed wood trying to clean it up as much as possible without making a dent or a flat spot. You don't have much wood thickness to play with, so if there is any heavy staining in those areas, there really isn't much you can do about it. This is one of the big problems with restoring old strippers that have been neglected. If they need more than just some surface scratch-filling and the wood is stained, it's nearly impossible to ever bring them back to look similar to how they looked when new.
Once the glass edge is feathered and the wood cleaned up as much as possible, a new patch of cloth is applied over the repair area using epoxy resin, and it's made big enough to cover the feathered area on the old glass as well as the bare spot. Then resin filler coats are added until the weave of the patch cloth disappears. Once it's all hardened, you can sand it smooth, feathering out the edges of the new patch. Follow this with a couple coats of a good UV-filtered marine varnish to protect the epoxy. It sounds like the entire hull could probably use a light sanding and some fresh varnish. Depending on your feathering ability, you should, at worst, have only a slightly raised area where the patch is, and at best, a pretty continuous smooth shape for the patch and surrounding area. Different resins have slightly different clarity and color, and old wood is usually darker than freshly sanded wood, so there is a pretty good chance that the patched area will be a bit different in color (lighter) than the original fiberglass was, but again, there isn't a lot you can do about it. If you're patching large areas that show when the boat's in the water, it may be a much better bet to paint the outside, rather than varnishing it. You lose the clear wood finish, but a good coat of paint often looks a lot nicer than a stripper with big patches and/or stains showing.
