The clouds used in the game are linked to a texture in which you can find in the 'Textures' folder of your media section. I don't think you can make them specific to one map, but you can make a sky specific to one map that kinda changes the hue of the clouds in the sky.. Not sure that's what you would like to do though.
I'll do some searching and if I find anything i'll edit this post and let you know.
~ Whisper