Have you got the clouds on a transparent layer? If so you should be able to do the following.
1. Add a layer mask to the drop shadow layer and make it totally black
2. Select all on your clouds layer and paste it on to your drop shadow mask.

That should do it. This is for gimp, but I think the steps are the same for photoshop.

Equally, I think photoshop has layer blending modes and allows you to set one layer to modify another? If so, you can set the drop shadow layer blending mode to darken only, and apply it to your clouds layer.