There is one good way to tell if it is surface rust or coming from behind. Get a small screw driver or a small pointed pick and try to push it through the middle of the rust spot. If it goes through, you need to cut it out and patch in a new piece. If it is solid, just touch it up with some touch it up paint.
If you have to paint that area, sand with 400 to 800 grit sandpaper using a block to keep everything smooth. Sand an area about 12" in each direction from where you want to paint. Then spray it with some duplicolor spray paint then paint it with some high quality clear. You can get a rattle can of extremely good clear at your auto paint store. Don't worry too much if the paint color is not perfect. When you clear over it the color mismatch will be minimal. Then do a good job buffing the over spray off so you get a nice even shine. The even shine is the most important thing to make it look good.
If it has gone all the way through, it would be expensive to fix at a shop. But don't get intimidated by that. I suggest getting a small mig welder off Facebook market place and get on YouTube and learn how to weld in a patch (it is just a series of small tack welds over and over until it is all sealed in), grind it smooth, go back to YouTube to learn how to bondo over the welds so it is nice and smooth, and paint it all up as described above.
The trick to smooth is to sand with a flat block until you start to see the metal or next layer of paint coming through. I really like to use my Dewault 1/4 sheet dual action sander or my Dewault 5" random orbital sander. Just keep the sander flat (don't sand on the edge, keep it flat to the surface) and it will make your body work flat.
When you see the next layer starting to become visible, stop. If you have a high spot (a shiny metal spot), make it a low spot and fill it with either a little bondo or high build primer. I sand my bondo with 60 grit to smooth, then hit it with 220 lightly, then paint it over with 3 coats of high build primer to fill in the scratches left by the sand paper, then block sand the primer with 400 grit and paint over that.
If anything rusts out again, you know how to fix it and have the tools to get er done.
Don't get frustrated. It does not matter how many times you have to re-bondo it to get it smooth. Just do it over and over again until it is right. Same with the paint. If you paint it and get a run, let it dry, sand it off, do it again. Paint it until it looks good.
Remember, there is nothing you can take apart or screw up that you cannot pay someone to fix. So far, I have not had to pay anyone to do anything over.