I was wondering how do I get my secondary sun to only light the terrain and not the clouds??
That is a good question. I would think rendering the atmosphere only with the primary sun, then rendering the terrain with both sunlights. I think the new version can alpha the atmosphere. Composite them in a photo editor.
There is probably a better, easier way.
I think njeneb's suggestion is the best way to try it, because at the moment it is not possible to selectivey "link" lights to objects or elements in the scene.
Martin