You can now assign different component shading groups for each of your render layers. Assume, for example that you have a plane on both layer one and layer two. In layer one, you can now assign half of its faces to a white shader and half of its faces to a blue shader. Then, in layer two, you can assign half of its faces to a green shader and half of its faces to a red shader.
To assign different component shading for each render layer
In this layer, you can assign component shading groups that are different from the first layer.