There are a few ways to get these areas taken care of. I apply a chemical stripper by brush, wait for the paint to bubble and then scrape it off with a putty knife and various scrapers. Sometimes it takes a few applications depending on how many layers of paint there are, but always wear long, heavy rubber gloves because that stuff burns very quickly when it comes into contact with skin. It's neutralized by rinsing off with lots of fresh water.
I follow this up by sanding by hand with 80 grit. I don't have a DA sander so I have to use elbow grease but I am sure some of the guys will suggest using a DA.
If there is any rust hiding there, use naval jelly and wire wool or a wire brush mounted to a reversible drill to get rid of it. When you have nothing but bright shiny metal, you're ready for a good coat of epoxy primer.
It's easiest to have your doors and trunk lid removed which will make these areas much more accessible, but I assume they probably are anyway if you are taking it down to bare metal for paint.
I bought a spot blasting gun to take care of the really tough or inaccessible spots, but I have yet to get it to work right, when I get it working it should make cleaning up seams and tight corners much quicker and easier.
Those are a few ideas anyway, I don't know that there is much of a rule to it, I just use whatever methods I have to to get that metal as clean as possible.
Hope that helps, I'm sure others will also give some input.
Rich