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I just did this exact repair on my boat a month ago. I hate cup holders.

I used heavy duty compound on a wool bonnet to get all the oxidation off where they were.

I taped over the back side of the holes with painters tape.

Mixed up 1/2 a tube of Locketite Marine Epoxy in white in a disposible container.

I used a disposible syringe like this:
https://www.amazon.com/Pack-Scientifi...7&th=1

Inject each hole, starting slowly in the deep part, working toward the surface.

Cover the filled hole with clear packing tape. You are looking to fill the hole as close as possible without under or over filling.

Let cure

Remove tape.

Sand as needed being careful not to sand the surrounding area.

It's a 95% match and as good as your going to get without spending $100 getting custom tinted gelcoat.

Questions?