Rain Channel Rust Fix?

I have rust, bare metal surface rust, in the rain channels above the
door on my beetle. The rest of the paint is great. It is chipping at
the edges, like this rust was painted over last time the car was
painted. I do have a quart of matching paint though, and I was
wondering if there was a way to fix the rust there, either by wire
wheel or by some kind of rust inhibitor, and use that paint as a touch
up, and then blend the clear coats together. Has anyone ever tried
something like this? I've never attempted body work, but it's something
I'm working into. Any suggestions would be greatly appreciated.