Although it looks hard, it's actually pretty easy. I'm not Continuum, but here's what I do
Just take the airbrush and paint the shapes. Restrain yourself to black, white, shades of gray, and dark brown (use opacity!). When painting a shiny metal surface, use only black, white, blue (for the sky), and brown (for the ground).
Set the painting layer on "Hard Light". For smaller details use the pencil or an airbrush with 1px radius.
Also, learn the basics of lighting and how it affects the material's surface (stone, metal, cloth, etc.).
For me, the painting is the easy part. The hardest part is finding the right art piece. Not everything fits into the game, no matter how good the paintover is.