How to touch up paint on figures?

Best advice I can give is to check out the tutorial section http://www.figurerealm.com/customtutorial
Proper preparation of the figure is a must, especially if you're going to be handling it on any sort of regular basis. Basically get an old toothbrush and use a soap and water solution to remove any dirt and oil from the figure, then at least a light sanding of the area to be painted. Re-wash and let dry before painting. Since you mentioned repainting the stripes on a Captain America, I'd suggest being prepared to repaint all the stripes rather than just one or two since color matching is an imprecise "science" most of the time. This goes quadruple for flesh tones, better just to repaint all exposed fleshy parts. It may look like an exact match, but you'll notice differences depending upon the lighting, better just to have all those parts with the same color to eliminate any doubt.