Skylights are not mentioned under the definition and examples of obstructed construction in NFPA 13.
Therefore we go with the unobstructed construction rules.
A skylight is considered a type of ceiling pocket in 13 (see the Skylights. section in the Installation Requirements chapter).
Before protecting in the pocket/skylight make sure it's even required. Is the depth of the pocket/skylight not exceeding 36 inches, 1000 cubic feet, the floor below completely protected by other sprinklers, separated from other skylights or pockets by 10 ft, quick response sprinklers used throughout the compartment? If none of that works, you can still omit sprinklers using the specific skylight rule if its area isn't more than 32 sq. ft.
Assuming you still need to protect in the skylight, unless the listing of the sprinkler permits otherwise, or you have fire modeling analysis done to permit lower deflector distances, you need to place the sprinkler 1-12" below the skylight.
However, under the unobstructed construction section, there is a rule that allows vertical changes in ceiling height up to 36 inches to be protected by a sprinkler at a different elevation. So you could have a sprinkler in a skylight under the "eave" of the slope 1-12" down from the ceiling part which is directly above the sprinkler, and it would still be considered protecting the highest point of the skylight as long as the highest point wasn't more than 36" above the sprinkler.