Yup. In the areas that the paint is still good, just faded or weak, you sand and prime. When you have it all covered with primer, hit it with 600 grit and paint it!
I meant to warn you against using something like Bondo on a working tractor. If you have no choice, you have no choice, but on a working piece of equipment it tends not to do very well with all the bouncing and jarring a tractor takes. Primer, or primer/filler will take care of rusty spots.
There is a much better alternative to Bondo, but I don't think they encourage it anymore. I'm sure you can find some YouTube videos on leading in holes though. That is a way more permanent method and doesn't rust, bust, or collect dust! Be very careful on breathing in the lead though. I'm hoping you don't have any holes like that.
George