Kristin,

I don't see a way to rotate skylights once they have been defined. I've
had this happen and left the angle alone but made sure the locations of
the skylights were close. You could probably do it if the visual
representation was that important. The skylights/windows are defined
relative to the coordinate system of the roof surface, which is in turn
relative to the coordinate system of the space. Your space probably has
an azimuth that is not at right angles to the rest of the building. You
could change the space azimuth, but then you would have to change the
vertices in the space polygon accordingly. If you're handy with trig you
could create a spreadsheet to do it for you and then copy the
coordinates into the input file - a lot of work.

Regards,

Bill