Basically, Inking is a more advanced process that requires you to get a feel for it. For this reason, I suggest you practice on some of the extra parts on the sprue, before inking a model. Here is a step-by-step method though.
1) paint the model as normal. Inking forms the deepest part of the shadow, so if you want multiple layers of shading, you should do some layering of your own. Highlighting at this stage is optional.
2) thin down your inks. Sometimes the inks are a little thick. For your first test, just use the ink as it comes out of the pot. You may find that thinner inks do better, and old inks will need to be "revitalized" as the water in them evaporates.
3) apply a LIGHT layer of ink to the surface you want to shade. You should apply this layer liberally. In your case, don't just pain the eyes and teeth of the Skull, but paint the entire thing over in inks. There's a reason for the Thin coat, and the coverage painting:
Inks sink into the recesses, but excess ink will lay on top of flat areas and form a stain. This can be good for thinks like power weapons or magic items, but bad for "real" light effects. You will find that the ink will slightly discolor the paint around it, so it's good to paint the whole helmet so that the change is even and consistent.
4) let dry for SEVERAL hours. Inks take a long time to dry, and only seconds to mess up. Make sure you have ample time after a wash, to let it dry completely.
5) repeat steps 3 and 4 until the shadows are acceptably dark. Remember: keep coats thin to avoid heavy staining.
6) clean up the model and highlight it if desired.
Good places for inks include: faces, chainmale, fur, fingers, armor creases, vents, and fine recessed detail (the script on GKs comes to mind)
Also- anything can become and Ink. Don't be fooled into buying GW inks or washes. You can thin down any water-solluble paint to an ink-like consistency. For dirty, black-washes I even use the water from my brush-cleaning cup. It worked wonders on my High Elf chainmail.