With the base colors of outline and solid fill selected, its easier to decide what ranges I want to use for a softer, graduated fill. Using the solid fill as a central tone and creating a Linear gradient with one highlight tone and one shadow tone, Ill replace each section of the solid fill with the gradient fill and then tweak it with the
Fill Transform Tool to suit both the shape of what Im filling in, the direction of light that I want, and any shadows cast by clothing, limbs, etc.