It can be done either way. I know body guys who wont put putty over bare metal even with the fillers they have now a days because they worry about adhesion to the bare metal. Then there are others, me included, who put it over bare metal thats been hit with a grinder and never encounter problems. 6 of one half a dozen of another really. Fix your obvious dents first then prime and block it. Chances are you are going to run into small dings, lows, and highs anyway and have to work it a little more then you can just spot prime those areas and re-sand them. If your having issues with surface rust from moisture in the air or what not go ahead and prime it then do your body work and then spot prime those areas again as mentioned above. Like I said it can be done either way. I'm sure there are others that will agree/disagree with me on this. Just my