As you may have surmised, and to answer your question, yes…the cloud layer is a second sphere. So the first sphere is the planet texture and the second sphere is the atmosphere effect, and the third sphere is the cloud layer. As I stated before, and as the others have said, the cloud and atmosphere layers must hug the planet tightly, like a second skin in order to look realistic. This can be done by simply duplicating the planet sphere and changing its size to 101%, that way you have a new sphere that is 1% bigger than the planet and centered perfectly on it. Then all you have to do is change the texture or material.
The next step is to make a bump map (not technically needed actually) and a specularity map to make the oceans shiny and the land not shiny. But play around with what you’ve learned so far and we can get to those later.