There's often an initial stage known as "flatting" where flat colors are applied, not necessarily to even serve as the final base colors but just to separate out all the individual elements on the page so they can be easily selected and worked on in isolation later. That process largely involves tracing around the outlines and then just clicking to fill the area with a solid block of color. Beyond that it's rather manual, very much like traditional materials, especially now that pressure and tilt sensitive stylus technology is readily available. The big benefit is of course being able to undo, make color corrections, etc. but the actual brush strokes and application of color is quite akin to regular old painting!