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if you don't feel like shading each individual layer, you can shade with a brown or violet over all layers. I usually set it to multiply and lessen the opacity. this is also the part where I will manually use a pen or airbrush to draw in the sections
just doing this process in a fairly old version of paint tool sai is still pretty simple. it took a bit of manual coloring to close off some sections in order to fill each one.
this part takes a bit more fiddling with the settings depending on what software you are using. the fill tool can actually detect gaps really well in CSP in my experience and can speed up the coloring process.