Best, easiest, fastest, cheapest way  depends on how deep they are. You should put some epoxy primer on first but its not mandatory. Then for deeply pitted metal you first use a thin bodied filler. It is sold under various names none of which I have committed to memory because I don’t buy them. I make my own by adding additional resin to regular body putty or bondo. Resin is sold at paint supply stores or the resin in a fiberglass patch kit is the same stuff. Add resin to bondo first and mix, then use the bondo hardener. If it "pulls up" behind whatever you use to smooth it leaving a rough surface you need more resin (pitch it and make another batch you don’t add resin to a batch already in the working stages or you'll have a mess to fix!) If it runs you overdid the resin, pitch and start over. Ordinary surfacer is used to finish the job with wet or dry sanding. Regular lacquer surfacers should not be used to fix deep pitting as the deep pockets do not dry for a long time and your nice smooth paint job will have  pits magically reappear in a few months. If you are wealthy enough to afford the two part surfacers you can pile it on as deep as you want.

 Guess I should have read the post better. My mix is for pits, not holes.