WElcome to the forum.
QUOTE; " the core is probably rotten."
Yep. OK, here goes.
For a small area, drilling holes,draining, and squeezing in epoxy
. You don't appear to be talking about a small area.
For a large area, define the edges and then cut the LOWER layer, in the cubby, from the under side. You may not be able to get the lower layer off in one piece. Then remove all the rotten soaking wet core. You do it from the V-berth so you don't mess up the deck.
Now, you need to make the cut out area as stiff as the rest of the deck. Applying layers of fiberglass
from underneath could be very messy. Consider replacing it with plywood
of the same stiffness or thickness. Glue in a patch, holding it in place with 2x4 struts up from the sole of the cubby. Consider whether bolting it through to the deck is needed. Cover the patch with whatever lines the cubby at present,or install a new ceiling.
Be sure in this process to find and plug
the way the water
got into the core in the first place.
Thee are other approaches that other forum members may be able to suggest. Think through what approach is best for you and your boat
Congratulations on your boat
and your new-found passion.