Once I anchor the skull using poster putty, using a desk lamp, I light the skull from the top left. This is simply how subjects of scientific illustrations are lit. Having a standard lighting direction means that those who are used to interpreting scientific illustrations will have an easy time understanding what shapes the shadows are indicating. If the lighting changes from illustration to illustration, one might have to think twice about whether a dark spot indicates a concave or convex shape.
I start by stippling the darkest areas of the skull. I can't go wrong in these areas. It's not a matter of mad dabbing of pen to paper. Each dot is actually placed with quick thought. When it comes to not-so-dark areas, I usually give a light sprinkling of dots over a large area, then go back in and put more dots where they are needed. When I first started learning how to stipple, I sometimes used a pencil to draw light isotopes, as if the skull were a topographical map, to help determine the concentration of dots to apply to paper. The inking portion of this illustration took 1 hour and 45 minutes.