If atmosphere contributes to noise in the clouds, it's usually only because of atmosphere between the cloud and the camera. Atmosphere between the cloud and the camera is most visible when the cloud is dark. So if you see more noise in the dark parts of the clouds than the bright parts, it's likely that you're seeing atmosphere rather than cloud, therefore the noise is in the atmosphere.
(Edit: You have to judge for yourself whether the bright parts are bright because of atmosphere or because they are actually the bright parts of the clouds.)
If in doubt, render some crop regions with different settings and see which chages improve the image quality for the least increase in render time.
Matt