I think you better work on the terrain and objects first and then add the sky as the slowest last bit. I have a love/hate relationship with the (awesome) clouds, and am hardly ever patient enough to work on them for hours.
Btw. make a black square in PS, white soft dot in center and point that towards the sun with a camera, as a (inverse) mask for a hole in the sky; easy spotlight, no moving around of SSS's needed.