Today I finished setting up my initial render layers and started setting up my nuke script.
I made 3 layers. Beauty, Shadow, and Occlusion.
When you make a new layer, nothing is in it and you have to add what you want in.
For the Beauty layer, I added everything from the master layer. Then I had to create some Layer Overrides on the primary visibility for some of the objects. Primary Visibility dictates what is rendered, the Layer Override lets you affect one layer, but not the rest.
Shadow Layer: Primary Visibility is off for everything except the ground plane, that is given the AiShadowMatte shader.
Occlusion Layer: All objects are given the AiAmbientOcclussion shader.
I am also currently having issues with the Alpha channel for this layer. The alpha includes the entire ground plane, not just the occlusion.