Not much to it really...the secret's probably in the size and position of the metaclouds.  Here's my method: 

Load the default spectral atmosphere (ie the one without clouds - or remove the default clouds if necessary). 
Rotate the ground down until it disapears. Add  in one or two metaclouds - of course ;-). 
 
Increase the size of the clouds until they are huge,** **then bring them really close  to the camera. Placing the camera inside a cloud a bit and to one side can work for dramatic stormy looking skies, with another metacloud overlapping but outside of the camera. 

I usually have to play around with them a bit - changing rotation, size and camera placement before I get the effect I want.  It's also possible to move, rotate and resize the individual sphere's which make up each metacloud!  

If anyone wants to get an idea of how big I make the clouds I can post a screenshot.

  I'd love to see your results. Happy rendering :-)