The blue sky and clouds are hard coded into the client and distributed on Gravity maps only. Naturally when you add a map your map it will have a black background. Nothing special to it.You need to hex your client to produce the sky and cloud effect.
I added my map to the server normally by adding the name to map_index & maps_athena, and updating my map_cache.dat. Nothing special about that. When I get to the wither part what i failed to explain was how wither was in fact a previous custom map that already replaced a gravity map that was hard coded to have the sky effect. So in order to get wither to have that, I simply replaced the name of the gravity map with wither and it obtained sky effects.
So to get a sky map you hex your client by replacing a Gravity map's name hard coded with the sky parameter (choose a map that you dont care about) and overwrite it with your own custom maps name.
PS: sky_tut was the proper map I used to demonstrate clouds. Sky tut (no underscore) is not a proper map and cannot be used as it has spaces between its name.