Create detailed line art to begin with. Make sure that you build all the details of your drawing in pencil first. This is important because the more detail you have in your line work, the greater the detail you can add when you begin applying your marker strokes.
Make sure that the line art that you have is completely finished. Erase any excess lines that you do not wish to keep. Be sure to run your eraser over the negative space (the areas without line marks) of the illustration to make sure smudges or fingerprints have been removed. You can ink the illustration if you want crisp lines or leave the pencil strokes if you want a more "handcrafted" feel to the illustration.
Color the base colors of each section of your illustration. Make sure to cover every single area that needs color. For instance, if you are coloring a figure in clothing, you will need to lay down a base color for the flesh, hair, and perhaps even multiple base colors for the clothing.
When selecting base colors be sure to pick colors that are not too bright and not too dark. These colors are sometimes known as "mid-tones." These colors can have shadows and highlights added to them later with ease.
Select colors that are a few shades darker than the base colors to create shadows on your marker rendering. Place these darker hues in places that light would have trouble reaching, such as just under a nose, or the inside of an ear. Do this for each element of your illustration.
If you like, you can add highlights using colored pencils. Select colors that are a few shades lighter than your base color and apply a small amount of highlight in the areas most exposed to light. These areas are commonly the top of a figure's head or the lip on a cup or chalice. Be careful not to add too many highlights or you will make the picture unrealistic.