Andreas Esau is working on an exciting add-on that will extend Blender painting with exciting features like layers. Check out his preview videos.
You may recognise Andreas at the creator of the Asset Sketcher add-on.
BPainter is a Painting Addon for Blender. The goal is to make painting in blender more efficient and less of a hazzle to setup.
In this video I demonstrate you how the Layersystem works in more detail. I have started to implement a powerfull management systems for layers in cycles.
As frontend you have a well known layerstack and in the background all cycles nodes are generated that are needed to enable this workflow.