Most of the time I make separate layers for color flats, shadows (with multiply-blending), highlights and line-work on top of everything else. Backgrounds basically get split up in a similar way, though often times go with a reduced layer set (e.g. no lines, like in the pic above). My coloring is pretty straight forward in most pics: flat base colors that get overlayed with shadow shapes (which can be filled with flat-colors or gradients). And usually I use one shadow color (and/or one base gradient) throughout the entire picture. Not sure what else to say here as there's really no "special magic" taking place. I hope this answers your question nonetheless.