You could either sand the rust areas and treat with a rust converters, or hit those spots with something like por 15, or if it looks like it is going to rust other places, take it down to metal and start again. For me, not having a show car, Por 15 over the whole thing was the cheap way to go, I guess it depends on how fancy you need this ride in the end, and what you plan to do with it. Others on here will have more detailed answers depending on what you want as a finished product. I was sort of under the impression that epoxy primer would seal out moister and keep the metal under if from future moisture issues, it might be that just the spots that are rusting is the only places the metal wasn't sealed up, or that rust was still on the frame when the epoxy primer went on.