I've finally found a method that works for dark clouds.
White clouds are easy enough: lay a strong wash, and before it dries out, wipe out areas in which you want to have puffy white clouds. I've found that if you start wiping when the paint is still quite wet, you get lovely soft results, with different shades of white and blue as the paint seeps back in.
But dark clouds have been a problem for me (see my last disastrous attempt). I finally found in one of my favourite books a way that works for me. The book is The Big Book of Painting Nature in Watercolor, by Ferdinand Petrie and John Shaw. The trick is to dampen the paper with a sponge and then apply the paint quickly. I used to apply water with a brush, which tends to make the paper too wet, and paint would whirl around rather than diffuse slowly through the paper. So using a sponge makes the paper just damp enough. This picture here is my first attempt, following a step by step guide from the book (I'm only at Step 1, obviously). I've used ultramarine, burnt sienna, cerulean blue and yellow ochre, just like it says in the book. What do you think?