How I've drudged over clouds... They were the most troublesome thing I've dealt with with backgrounds, getting clouds to look good. And accidentally stumbled across a was able to get them looking good. XD Starting with a very cartoonish line-art. And then taking a new layer under that line-art, your brush being say the 3rd from the bottom preset brush, set opacity to 45%, flow 68%, and multiply with a tinted grey colour, relevant to the pictures colours.
the atmosphere glow was super fun to do, but the clouds were a pain. 
