If the areas are small finish AND then use colored wax sticks (Mohawk is one brand) that match the final color you end up with.

It is very difficult to get any filler to stain to match finished wood with a clear finish if the wood has ANY figure (AKA 'grain').

It takes many attempts with multiple colors and mixing and then finishing completely since a 'clear' topcoat can subtly alter the color of the filler and wood differently, making the patches stand out badly.

Minwax high Performance Wood Filler works well under paint.

You can make invisible repairs relatively easily under paint.

brickeyee, thanks for your reply. I think I'm just gonna paint these stools and save the dye for something else that might come along down the road. I love the colors capable with the Keda dyes.