You should prepare and repaint the entire window unit. Begin by removing all loose paint with a wire brush or scraper. Don’t forget the ends and underside of the sill, as peeling or cracking often begins there. Next, remove any old caulking from the joints in the frame and the areas where the frame meets the sill and where the frame and sill meet the siding. Finish the surface prep by sanding the wood until it has a bright, new look. This removes any decayed wood fibers from the surface and provides a sound surface to paint. Now apply one coat of Undercoater 450, again paying special attention to the end grain and underside of the sill.
After the primer dries, apply an acrylic latex caulk to the joints in the frame, the space between the frame and sill, and the space between the window and the siding. Follow with two coats of a top-quality acrylic latex satin or gloss house paint, like Kem Gloss. After you replace the storm window, make sure the drain holes at the bottom are open. This will prevent the condensation that builds up on the inside of the window from collecting on the sill.