Build your colors gradually, and layer them. Apply a light undertone, and build darker colors slowly on top. Crayons can actually be more difficult to layer with due to the high wax content. Don't confuse them with colored pencils! If you want the "look" colored pencil, just use that instead.
The idea is to fill an area by coloring the fabric behind the embroidery. Usually, this means that only the outline is embroidered, with some details added. However, tinting isn't only for coloring inside the lines. Many artists use this technique to create spectacular backgrounds, borders, and accents for their embroidery work.