There's many ways to paint clouds. For a muted morning cloud sketch, I like to start off with toning the paper with a pitt graphite stick. After rubbing in the graphite, the paper has a nice dusty background to work with.
My kneaded eraser works wonder with highlighting the clouds. A touch of blue pastel indicates the space between the clouds. Just two shades of blue & grey saids it all. I like to add a little color with my color pencils. I love painting clouds cause there's no right or wrong way to do it.