I have been filling up seams on my Nick S Stitch and glue. I have been using a random mix of ground up saw dust and white micro balloons (and epoxy). My only regret is that I have been mixing up potions inconsistently. Some of my lighter brews are noticeable and stand out if you look at them from 6".

My retrospective tip would be if you are going to splodge much of this stuff around it may be a good idea to mix up a good quantity of dry ingredients. That way you could at least retain some quality assurance.

For red meranti plywood, I guess a good mix (for me) is about 45% microballoons - 55% ground saw dust.

Maybe practice a little with your mix. Sanding artificially lightens the dookie schmooze which then darkens to about its original wet colour when you epoxy over it.

Other people have suggested filling stitching/staple holes with a sliver of construction wood sharpened in a pencil sharpener. Jam it in with a little glue then trim it off. I think that maybe the best idea for hole filling (although I haven't tried it).

Good luck.