The way I do it (and its not the only way) is to make a single cloud layer go up to, say, 30,000 ft. This is usually higher than I will fly (I fly single-engine props mostly) and then have other cloud layers on top of that, so I rarely see the division line. Also, making the bottom layers thicker than the ones on top kind of solves the issue. Just play around with the settings a lot until you find something suitable. (Yeah, I know, its the answer to everything--play around with it!

)