When I built my strip canoe, I used Durham's Water Putty as instructed in Gil Gilpatrick's book "Building a Strip Canoe". I discovered it is a very pale yellow color and it did not match the dark cedar I used to strip the canoe. So I used aniline dyes to color it which worked quite well. Aniline dyes are a water-soluble powdered dye available at wood working supply houses. It took very little dye to color the putty, 1/8 teaspoon per 4 tablespoons of putty. Dissolve the dye in a little water before adding it to the putty or color streaks will appear. I smeared the whole hull with the putty using a green ScotchBright pad and then after it set I sanded back down to the wood. It filled every staple hole but it took a lot of sanding to get back down to the wood. Contractor supply houses carry Durham's. It comes in a round red fiberboard can with a pry-off lid.

The perimeter of the staple holes still darken from wetting with epoxy. They will still show no matter how well you color match the putty. I left the tight knots in the strips to give the hull a woodier look and this color texture makes the dark holes less obvious. Most people don't notice the holes when they admire all the natural wood.

If you chose not to putty, you may want to do a seal coat before glassing to limit the number of little bubbles that will form in unputtied holes.

Staples or no staples, putty or no putty, it's an effort versus aesthetics choice.