If it's a big divot where there should be material, then yeah, you just apply another batch of Bondo. If there's unevenness, it is up to your eye to figure out if it would be better fixed by adding more material, or by sanding what is there down smooth.
little holes, aka pinhole-flaws are not all that easily fixed with pure Bondo. Bondo is thick, like cake frosting. To fill in pinhole flaws, you ideally want something thinner, that is formulated to seep into tiny spots. You also want something that isn't going to shrink too much, or it will just settle into the holes and shrink into little divots, forcing you to apply a second coat. Most surfacing-primer paints have this problem. Don't fall into the "I just need to add one more coat" trap.
Almost anything you use must be physically worked into the surface, otherwise, the pinholes will just trap air and prevent your filler of choice from seeping in. This is done with a coarse bristled brush, a rubber squedgie tool, a plastic scraper, a putty knife, or just a gloved finger.
Bondo markets a special spot filler putty, but it doesn't really blow me away. I've had decent luck both with mixing bondo and polyester resin, and to a lesser extent using jointing compound.
Whatever you use, it is useful for it to be a different color than the resin you've applied. That way, you can be sure if you're sanding off your filler layer, or if you've cut through to the main layer. I do this with powdered pigments, since they mix with anything. If using bondo, since the catalyst has red pigment in it, and you mix it by eyeball, almost every batch you mix up will have a slightly different color already.
If all you have is pinhole flaws (which probably won't be the case, but just imagine it), you'll apply a thin solid layer of your filler material and gently sand almost all of it off once it has cured. You should see just your original (usually pink) bondo layer, followed by speckles of filler where there was previously pinholes. Since they're just speckles of filler, it doesn't need to be strong, it just needs to take up space.
If you sand too aggressively, you risk popping the filler right out of the flaw, just like taffy pulling a filling out of your teeth.