Ah, I gotcha. Well, almost all of my coloring/shading is done in a folder with a mask on it, so I don't have to worry about accidentally coloring outside of the linework. After that, I make a 50% grey layer behind it to check my colors.
From there I use the polyline and fill tool for my solid colors. After that, I make a layer above it for shading. After figuring out where I want the light to come from, I use the polyline tool again to create the dark areas. I usually fill it with slightly desaturated blues, purples, and reds. Then I set the layer to a blend mode, either multiply, linear burn, or color burn, and then adjust the transparency. Same deal on a new layer for larger light patches, except I'll use orange or yellows and set the layer to overlay or add glow. Sometimes, like in that picture, I will blend the lighter layers. The pure highlights face the light source, running in the direction of the length of whatever bodypart.
As an aside, I will say that this is probably one of my least favorite drawings, both in coloring and the figures themselves. I've been trying to keep colors simpler and bodies more appropriate to the artstyle since.