This particular hole was a miss drilled gas cap hole so it is horizontal instead of vertical. Most of what you will see will apply to vertical gauge holes. I cut a circular plug out of 1/8 inch luan and the first pic you can see it is jellied in from the bottom. The second pic shows the plug from the top. You can see the balsa core of the deck around the perimeter. Next I cut cloth then put four layers in with resin. The idea here is that the resin will permeate the balsa core for a strong bond. if you just put pure resin in a space like this it will be brittle and crack like window glass. Cloth is very important. More to follow when the resin cures.
While the resin is curing the difference between this hole and a vertical hole is that instead of a thin plug you should use a plug slightly thinner than the hole and do both sides with jelly. If you want to fill a 1/2" bolt hole in a transom find a 3/8" dowel and cut it slightly shorter than the thickness of the transom and wrap it with resin impregnated cloth and shove it in. Then finish the ends as explained later in this thread.
Bottom side sanded. top side jelly in. This is where it is the same as a vertical dash. Sanding next.
I sanded and layed some bondo. Then I re-drilled the hole. sorry about the double pic. What you see on the right is original deck core. On the left is from bottom to top you see jelly, luan fill wood, glass, original deck glass, and my work.