Option 1:
If you are going to fill gaps with an epoxy/sanding dust mix, the best results are to first put a sealer epoxy coat on the wood to prevent stains around the areas that are filled.

Filling gaps usually only takes a few tablespoons of epoxy, so this is NOT the time to try to save epoxy. Get some tiny measures (bottle caps or whatever) and get the 2-1 mix right.

For color match, generally, a mix of 1/3 each of silica powder, sanding dust and wheat flour (the ordinary kitchen stuff) will be slightly darker than the gap being filled, which is exactly what you want. Lighter filler shows more. Dark is better.

The second option is to fill with a water based wood filler before any epoxy work. Duram's is a good one. Just make sure that it's not lighter than your wood.

John