I assume you're talking about the quarter windows. Those pieces of glass is held in by urethane caulk. You'll first have to cut the glass out before doing any rust repair or welding in those areas. First order of business is to remove the outside trim around the glass.
I'm sure the seals are brittle and the glass is probably pulling away...which will help with easier removal.
Using a combination of utility knife and a sharpened putty knife, you can start cutting the seal from the inside of the car.
There is a tool available for that task as well. You can find them on this site.
http://aegistools.com/
As for a patch panel for the rear lower quarter, you'll either have to cut one out of a donor/parts car, or fab a piece using 20 ga. sheetmetal. No one really makes one...however, you might be able to modify one from an El Camino.
Welcome aboard! You might also want to tell us about your ride and your plans for it.