Can we render a sky layer with transparent layers? I am using a transparent alpha in the shading menu, while rendering my layers, so I can later composite them together. 


Question is, is there something like a sky layer that would go on the bottom?


Possible fork of this question - 2. is there another way of compositing two layers on top of each other? Can I pull an alpha from a layer with the transparent option off?
The easiest solution to this is to do a third render without any visible objects and Alpha set to Sky in the shading properties in the render menu. Once that's done, alpha over your sky background just like you have done already between the two scenes.