The main considerations with using body fillers and stopping rust are are:
1. all sides of the metal can/will rust if exposed to any air/water
2. you want to grind/buff/sand/media-blast to shiney metal on all sides
3. you need to seal all sides of the metal with a water/moisture-proof sealant - a 2-part epoxy primer - is the best choice for sealing the metal
4. body filler (compatible with the primer) is used over the epoxy primer
5. sand
6. if any metal shows after sanding, you need to cover with another epoxy coat
7. maybe someone will comment on sander-surfacer coats
8. someone will correct and/or add-to/clarify the brief items in this list
Maybe someone will post a link to a good tutorial on the Internet?
