1. Open your Line Art image. (Bear with me and pretend this is your line art.) ;o)

2. In the File menu, choose Clone. Save the Clone/copy with a new file name, then close the original Line Art image to leave it unaltered.

3. Working on the renamed copy of your original Line Art image, Select, All 
(or Ctrl/Command+A), hold down the Alt key, and click twice somewhere on the image with the Layer Adjuster tool. This makes duplicates of the Line Art on two Layers.

4. In the Layers list, double-click the upper duplicate Layer and rename it 
"Gap Repair". Then double-click the lower duplicate Layer and rename it 
"Master Line Art". 

5. Click to close the "Master Line Art" Layer's Eye Icon and Lock Icon.

6. Close the Canvas' Eye Icon.

7. With the "Gap Repair" Layer highlighted in the Layers list, zoom in and, using one of the Pen Brush variants, paint with black to close gaps in the areas that will be filled with separate colors. Be sure to paint these gap repair lines so that their inner edges define the Filled color outer edges exactly where you want them to be. 

8. With the "Gap Repair" Layer still highlighted in the Layers list, in the Select menu, use Auto Select, Using: Image Luminance, then in the Select menu, choose Save Selection and accept New. (This is named New Mask 1.)

9. Click to close the "Gap Repair" Layer's Eye Icon and Lock Icon.

10. With the Selection still active (a double row of marching ants all around the line work), click Canvas in the Layers list to highlight it then click the Eye Icon to open the Canvas.

11. Double-click the Paint Bucket tool to open the Mask Threshold dialog box, move the Mask Threshold slider to 50%, then click the OK button. 

12. With the Paint Bucket tool still active, in the Controls:Paint Bucket palette, choose Cartoon Cel from the What to Fill: drop down list and Current Color from the Fill With: drop down list.

13. Choose a color, then click in one of the enclosed areas with the Paint Bucket tool to Fill it. 

14. Zoom in to check the edges and if they're not solid color all the way up to the black lines, adjust the Mask Threshold slider by moving it slightly to the left, then click with the Paint Bucket tool again, in the same enclosed area to Fill it. (The more to the left the Mask Threshold slider is moved, the greater the area that's filled. 
If it's moved all the way to the left, it may fill the entire Canvas, past the lines.)

15. Once the Mask Threshold is set and the first enclosed area is filled properly, choose another color and Fill the next enclosed area. Continue until all of your enclosed areas are filled with color.

16. Use Ctrl/Command+D to deselect the Selection.

17. Zoom in and check the color where it filled in the line gaps. If you notice that a few of the pixels are grey or black, click the Pen brush, choose the 1-pixel variant, use Ctrl/Command+Click to pick the Fill color, and click the grey or black pixels to change them to the appropriate color. If the filled gap doesn't quite align with the outside of your black lines, paint in the pixels to make it align. This should be very minor touch up if you painted in the black line gaps carefully in Step 7.

NOTE: You may also notice that, where the color filled the enclosed areas, some of the black lines' edges are looking pretty scrappy. Don't worry about that. Just do the next step and they'll look fine again.

18. In the Layers list, highlight the "Master Line Art" Layer and click the Eye Icon and Lock Icon to open them. The background will be white. This is another thing not to worry about. Just do the next step.

19. Click the Layer Adjuster tool and, in the Controls: Adjuster palette, choose Multiply from the Composite Method drop down list. This makes the "Master Line Art" Layer's white background transparent so you can see the colored Canvas.

Now your original clean black line work is covering any flaws made in the line work on the Canvas due to filling with color. Your underlying color work is all done and you can proceed to add highlights by whatever method works best for you. It could be by making selections on new Layers and filling them, or it could be by painting on new Layers. Whatever works for you is the best way.

Let me know if this method helps you get your work done faster and especially if you find anything in the tutorial that needs fixing. Thanks, and...