Filling holes is a two stage process. The first is to wet out the hole with straight epoxy. This can be done with a putty knife or one of a number of tools. Mash it in the hole using the blade to force it in. Capillary action will cause it to seek out the very corners within it. The idea is to wet the inside of the hole, priming it for the filling. Wait a few minutes for the goo to soak in as you mix a thickened batch and go over the hole again, mashing it in hard with the knife, plastic applicator, etc. Smear this off dead flush with the surface or just a little shy of flush. This is the first stage. When the goo has kicked off, mix up a fairing compound and apply a slightly proud puddle over the hole. This is the second stage and what you will sand flush with the surrounding surfaces.
I dislike warming epoxy and applying it to a cooler surface. This just warms up the open cells in the wood and the air in them, which form bubbles that will rise to the surface and make pin holes. I do it the other way, by warming the wood. This causes the gases in the cells to expand a bit. Then I remove the heat and apply the goo. The cooler epoxy causes the air in the cells to contract, which causes the epoxy to get sucked into the cells and no bubbles. I also try to insure there's a shallow dimple at the top of the hole, so the fairing compound has a divot to get a hold of, when it's applied. Some will tell you all this can be done in one shot, but I've never been able to do it reliably, so I just assume there's going to be slight divots over each and top them off later, with something easy to sand.
Lastly, decide on what the hole needs to do. If it's part of a structural element, use a structural filler to initially fill the hole. This will retain the integrity of the area around it, if compression/tension loads try to distort the hole. If the hole is just a cosmetic consideration, then fill it with a fairing compound. For example around chain plates or other hardware attachments, I'll use a structural mix to fill the hole, but if it's a few temporary holes where a butt block or scarf was held until it cured, then fairing compound.