I think the question was about a multiple skyboxes case.
That was my main question but the answer does infer that there are at least 2 levels to work with: the skybox and the sky background itself. Time to start messing around with it an see. Thanks for the responses.
It's very common for places to have two or more light sources. In fact, almost every light source has more than one. Why? Each map (Blizzard map - custom ones should too) has a kind of default skybox. When you open the Light.dbc and see a row with lots of 0's in those first few columns, it's often because that's the default skybox for that map. Every other map entry is covered by both that entry PLUS the default skybox. That's where my comment earlier about transparent skyboxes came from and Skarn indicates that shouldn't be a problem.
Look at this screenshot I made from Lightmapper:
http://i.imgur.com/T076wQx.png It's showing you Dreadmist peak. Dreadmist peak is the smaller, completely black circle in the middle. That's got its own Skybox settings. It's also within the circle for the Skybox that basically covers Crossroads. They're both covered by the general Skybox for Kalimdor.
So Dreadmist peak is covered by 3 Skybox settings.
