On Kymaera, you edit all skins on a horizontal monitor. The vertical skins appear vertical in the skin editor. When Kymaera is run in rotated mode, it then rotates the entire skin to the correct 90 or 270 degree orientation. This way, I don't have to worry about rotating mouse clicks or events.
The downside of this is: you probably have to create the skins on a different computer than the one you're going to run it on.
-PMF