Simply use the painted shader as normal as a "blend by shader" part. Under that should be a check box for "Invert blendshader". That should do it. Then simply paint as you said, painting where you don't want clouds.
This is often useful for me when doing things like paths. I use the paint shader of the path for dirt, rocks, etc. Then I invert it and use the other one for grass, tree, etc populations.