You will discover that wood sands a lot faster than epoxy. You should strive to leave the epoxy in the holes a micron shy of flush. Then you can quickly sand the wood down to the level of the epoxy in the holes. Otherwise, you may sand a donut shaped depression around the fills.
Another option would be to go ahead and epoxy the whole boat, then finish filling the holes with thickened or unthickened epoxy. At that point, a cabinet scraper will bring the fills flush quickly with minimal sanding to clean up.
Hooper