2 issues I ran into with my next project: 1 - get the sky to show through in the compositor and 2 - get solid objects inside a transparent object to render properly in the compositor. Issue 1 - make a composite layer with just the sky and groundplane and enable "sky". Turn off sky on all the other layers. 2 - Create a mask layer of the solid on the transparent object layer. This way you won't see the backside of the transparent object on the front of the solid. Don't try to fix it in the compositor.

Cheers