But he's EVIL!
This is probably the biggest help right here. Layers help with the coloring (software like GIMP is the go-to here, if you're on a budget), and also with shading. You stick the line drawing on one layer, put the colors on a second layer (or one for each color, if you so feel), and the shading on a third layer. Set the top two layers to multiply. This means that the black lines of the drawing will "bleed through" to the top, and when you color, it'll allow you to brush close in. It also means that if you use a single color (gray) on the shadows layer, it'll automatically darken the colors beneath, so you don't have to figure out what to use for shading.