Proper Curb Mount Skylight Flashing
Here is a very good example of roof flashing around curb mount skylights. Curb mount skylights are designed for roof slopes of dead level to 60 degrees. This application is on a porch roof with a slope of 2/12. 
You can see a waterproof membrane is installed from the top of the 2×6 frame, down on to the roof deck, then 6×6 metal flashing is installed. 
The shingles are installed to manufactures specifications, as the shingles are cut around the sky light openings 6×6 tins are installed, this is called step flashing.
After the shingles are ran, the step flashing is capped with counter flashing.
Then the sky lights are installed. When done properly this is a water tight application.
