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I color in a bit of a weird way in Illustrator. After I've finished the linework, I make a new layer and just make a shape using the pen tool with the color I want underneath the lineart, and fill all of the lines that way.
I use the pen tool to trace over a pencil sketch with a path with stroke of 3 or 4px, depending on the size of the image. After I'm done tracing I'll take the Width tool and vary the size of the lineart in some places to that there's some variation in line thickness.
Once I'm done with all of that then I'll play around to find a good color for the lineart, cause plain black usually isn't very interesting
For fading colors I use the gradient tool with two similar colors with different tone. Gradients are kinda awkward to work with in illustrator, so you may want to look up a tutorial on how to use them.
For regular shading I'll just draw a darker shape with the pen tool on top of the flat color that I'm trying to shade.