It’s more efficient to use widely available Color Putty or similar product to fill small nail or brad holes in furniture after the sealer coat has been applied than it is to use wood putty before applying the stain and finish.
There are three reasons.
First, using Color Putty after the sealer coat but before the topcoat is much faster. With a little putty on your finger, you can move from one hole to the next very quickly, wiping off the excess as you go.
Second, you don’t have to wait for the putty to dry before sanding smooth as you do with either water-based or solvent-based wood putty.
Third, you have a much better idea of the matching color to use after you have applied a coat of finish than you do on the raw wood before applying a stain or finish.