Start adding color to layers below the "LineArt" layer. Working on multiple layers when adding color will allow you to easily, make revisions later on if needed.

The color will be viewed through the black line work, so using light, intense colors will probably give the best results. Also your eye is going to mix the color of the line work with the under lying color, and sometimes this can cause problems. For instance, yellow viewed through black line art will look green, instead of brown, which is probably the desired color.

Rule of thumb: Keep underlying colors light and bright.