I agree with Mike.
Most of the time, unless the shot calls for flying through it, doing bg plates separatly of clouds, god-ray efects, distant smoke plumes, birds, etc. are the way to go using 2d applications, to paint, and animate as a separate plate to combine, and color-grade with your shots
I have a HUGE bg plate of a sky in the download section if you want to use it as a layer to customize your own sky to test with.
Just fyi, our download section is growing a LOT, so take a look, and grab all the free stuff that you can!
Israel "Izzy" Long
Motion and Title Design for Broadcast-Film-DS