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.