One thing I do to help me do the flat coloring at least is on the coloring layer, use the magic wand tool to select all of the sections that are gonna be the same base color, expand the selection by three pixels, fill with the bucket tool, and deselect.
And to make that go by easier, I made an action script to do the expansion, filling, deselection, and then create the layers with the blending filters I like to use for shading and highlights.
And then for the shading and highlights, I do still have to find the right colors to use with trial and error, but eventually, usually, after only about 20 seconds, I find them