Should I Fill Knots Before Staining?

Open knots or checks, large or small, are actually the easiest to fix as they are already a visible and accepted defect. Because these knots are darker than the surrounding wood, filling them with a matching or darker color is typically all that's needed.

Do I fill wood first or stain?

Make sure you fill the holes before staining the entire piece. Push the filler or putty into the holes with a putty knife and smooth it out slightly over where you want it to be so you can sand it down to smooth. Then stain the rest of the piece as usual.

Does stain soak into epoxy?

In theory, yes, you can stain epoxy wood filler. You use a gel stain to apply over the epoxy wood filler once it has hardened. The trouble is that this isn't a real stain at all, in fact, epoxy is plastic and just like every other plastic you've ever worked with – it can't absorb the color from the stain solution.