First, make sure they are dry inside beofre sealing them.

Easiest is to fill with 3m caulk and run a screw in them.

Cleanest look would be to fill with marine tex and then gel coat over with the factory gel.

If you only have the gel and no marine tex you can thicken the gelcoat with talc powder and force that in the hole like you would the marine tex, then fill the outside with straight gelcoat.