This is how I do it- Cel Shading in Harmony
As you can see I use a combination of Tone, Glow, Blending and Cutter effects. I frequently get confused.
As far as animating these shadows all you need is a brush or pencil tool with a size of 1 or 2 and a draft layer. Animate carfully and apply the effects like you would any other frame by frame animation. Just take it one frame at a time and plan carefully.