I am trying to figure out how to work with render layers. Now I have two render layers connected to the output via Alpha Over node. But when I render the composite output layer is not the combined output of the two separate render layers. What is my stupidity?
It could be that you are not actually providing the compositor with any transparency. The alpha output socket from the scene node will just be a solid white unless you check the following properties:
Blender Internal: Turn on Shading > alpha > transparent, in render properties.
Cycles: Turn on film > transparent, in render properties.