Inspect the roof, when closed, looking for cracks or holes.
Remove the old caulking, using a plastic scraper. Scrape any excess caulking off the roof.
Wash the area with mild soap and water and clean rags. Let the area air-dry.
Apply new sealant with a caulk gun. Put caulking along the seams of the roof. Wipe off any excess sealant.
Remove screws if the leaking is around the screw holes. Add sealant to the hole and replace with a screw that is larger than the original, using a screwdriver.