Fixing rust are we?
Get rid of as much as possible, prime with rust killer/preventer, and have fun with the old Bondo.
Before you prime the Bondo, make sure it's glass smooth. Last time I used it, I though I had the Bondo smooth, after priming, I realized I didn't get it as smooth as I thought. Wow, that's a long sentence with a lot of I's.
The smoother you get the Bondo on the first application the better, unless you like sanding.
If you're trying to touch up those areas, it's better not to tape a line directly around it, you'll see it plain as day. But do tape off the obvious other things, like the tires.
A little overspray generally won't harm much, and it will probably buff right off.
I think we all need to see before and after pics.
I forgot to when I did mine. Both of the corners on my rear bumper and the cladding just in front of the rear wheels were down to black. I spent several hours wet sanding, priming and painting. The after pics are in the link on my sig.
Good luck. I hope you like the scent of lacquer based paint.
