Here is another flashing where the covering material is half way on the flashing.  The roll is carefully cut around the cup to seal completely.

Here a skylight still on the curb shows the base sheet almost full covering the outside of the curb in preparation for the material.

Now the top layer is being installed and the material is lipped up the curb to provide a uncut continuation of material to the top of the curb. 

You can see the modified attached to the top of the curb.  With the material rising to this edge, the lip of the skylight will overlap the material attached to form a solid seal keeping water out.