If you have a large spot to repair and have to cut away the fiberglass, cut the glass from the inside rather than the topsides. This way the repair will be hidden by the ceiling instead of messing up your topside.
I would drill a 1/2" hole on the inside about in the centre of the damaged area, taking care to drill through only the fiberglass. You can then use a straightened coat hanger (is there anything they can't do?) to probe the extent of the rot.
Using a router, cut through the fiberglass and just into the rotted wood with a 1/4" bit. Take this out roughly with a chisel. You don't need to get to the topside layer of glass at this stage. Once that is done, the next part will test your mettle. Make a float for the router ( a float allows the router bit to span an open area without changing it's depth) and set the bit just shy of the topside glass. Clean out all the rotted wood. Do this one more time, only with the bit set to the depth of the topside glass.
OK, heart attack time is over. Cut a piece of Baltic birch plywood ( or whatever marine grade you can get. We're interested in lots of plys, the glue holding it together is irrelevant) for the patch and soak coat it in epoxy.
You can put the patch in now but it's messy. Let it dry, scuff it up for some tooth and epoxy it to the bottom of the topside glass.
Finish the patch with glass. Of course you will need to bevel out the repair and place ever larger patches of glass in until you're back to ceiling thickness.
It sounds worst than it is.
Oh, on the float, don't make it too big. Just enough that wherever you are on the rotted area, the float is on a stable surface. If it's too big, it will start following the curves of the topside that you might not want.
HTH,
Frank