If you're going to apply Bondo, start with 80 grit. Remove all the loose paint surrounding the rust spots first. You'll need to grind ALL the rust out, so if it's really heavy rust, you might need a grinder with a 36 grit disc attached. Do you have any bodywork tools, or can you borrow some? Take your time grinding on the panel--you don't want to warp it from excess heat. The area should be nice and shiny, and the old paint should be ground as well. If you look at the roof from the side, the old paint should taper down into the freshly-ground area. That's what Milque meant by "feather-edging". You'll need to feather the paint a few inches from the bare metal areas. Bondo will not adhere to smooth old paint.
You'll need some Bondo spreaders and some hardener, too. (Insert standard Viagra joke here) Follow the directions on the Bondo can explicitly. If you mix too much hardener, it will make the Bondo shrink and crack down the road. If you use too little hardener, the Bondo will never cure. Use as little Bondo as you can. If you pile a lot on the roof, you'll spend forever taking it off. You can always add more. Once you are satisfied with the height of the Bondo, use 80 grit to shape it. Then you can go down (up?) the sandpaper order until you are happy with the shape of the filler. 220 is a good point apply primer. You can also use putty that's available in a squeeze tube to fill minor nick and gouges before applying primer.
Milque pretty much covered the rest. Just make sure that you tape EVERYTHING that you don't want paint on.