SWG's and Vurt's are already mixed, apparently.
All you need to do is backup your current skies and replace each one. If they do look weird, you can go back to what you had before. I've done a lot of overlaying of texture replacers after installing MGSO. For me, it's a fantastic base, so when I see something I like better, I just install on top. Skies are really no different than any other textures, if you like AOF's night skies, but Vurt's day, or vice-versa, you should be able to use both.