RE: General building Q, how to fill a low spot
In this situation I would use a 1:4 epoxy/microballoons mix, or some sandable balsa filler. I have heard mixing spackle with elmers wood glue (5:1) makes a good balsa filler if you don't have any. If it is a larger depression, you could glue balsa, sand, then fill in the rest with a filler.
The goal is to get it pretty good in the bare wood stage. You can use Bondo glazing and spot putty to fill in any remaining imperfections after you've glassed it.
-ron