Many skylights used in metal roofing follow a very similar design. The skylight, or "light-admitting portion," is framed within a lip. The lip then rests upon the roofing in order to firmly lock the skylight in place. Some designs may also come equipped with a "retaining ring," which acts as a form of gasket to keep moisture and/or water flow out of the light.
Like with all skylights, you have to form a seal in order to ensure that it is waterproof. The standard method for doing this with metal roofs is caulking. Special diligence must be paid to the "back pan" of the skylight, which has slightly different features than the rest of the design. Often, this must be secured with silicon before the shingling or standing seam metal roofing is placed upon it.
There are two basic types of metal roofing: standing seam and shingled. Skylights are typically made more difficult by the long pieces offered by standing seam design, especially if your roof has intricate or diverse contours or shapes. It is significantly easier to use shingling, as this can be altered to fit the specifics of your roof and skylight placement.