In the first image, what is shown in the screenshot is my default layering plan. I always keep it simple and within minimalist order. The base colour which is the main 'fill' always stays near the bottom, the shadow colour just comes above to provide dark areas of the scene or character. Finally the light colour layer tops them both, as brighter colours highlight areas sharply and are more powerful when on top.
The Ink layer must always remain ahead of all colour layers to keep them within each object. A few times I have coloured the entire screen in black, then reduced the opacity down to provide a rich, darker atmosphere to a scene. It helps enhance the audience's understanding, notifying them whether it is night time, or enclosed in a dark spacing. I also did the opposite to light scenes set in the day, just to give it a more uplifting feeling.
Key:
b - base colour
s - shadow colour
l - light colour
ink - final black inklines
