OK, so if you take a sphere spinning on its axis and put it in a spherical aquarium I could see it all spinning together. But what I don't see is how that work

OK, so if you take a sphere spinning on its axis and put it in a spherical aquarium I could see it all spinning together. But what I don't see is how that works in an atmosphere which is mostly near the earth's surface. It seems like you would lose a lot of energy as you entered the stratosphere because the air density increasingly falls, there's less room for friction to cohere the atmosphere. High clouds should be less effected which would make them appear to move much faster than low clouds. Is there a good source somewhere on how this works that takes this into account? The stuff I've seen just assumes its own model and works backwards.