I use adobe photoshop for everything.
Here is the basic way I do this:
1. Make a rough sketch.
2. Redefine the sketch and create the actual Ink.
3. Fill in the colors with a basic color, like for a skull fill it gray
4. Add a dark tone layer, for the skull add a dark gray
5. Add a bright layer, for the skull bright gray.
And keep repeating this until finished.
It just takes time, patience, and practice.
If it makes things any better it takes me more time to ink the actual illustration then to color it.