IIRC, you can create a new shader for your custom sky (just copy one from skies.shader in the scripts\ dir) place it into your own .shader file (mymapname.shader for example - you would need to add this to the shaderlist.txt file though). Then just edit the the q3map_sun (i think) value in your sky shader. There's a description of how those values work in the skies.shader file comments somwhere.

Hope that helps, sorry i can't be more specific, but I don't have the editing tools/files installed atm.