The multiply method, for me, has been a nice shortcut for shading. When coloring characters with a lot of variance in color, it's a godsend. Selecting a darker color in the first place is fine. Each time you get to another color though, you have to change it, and make sure it matches the previous shade, which takes just a little bit more time. Using multiply and just one shade of color eliminates having to worry about that. Hope that answered your question, I can try explaining it better if it didn't.
I see you color your lines by hand. To save time, since it's on it's own layer, you can color them all at once. Select the lineart layer and then open up Hue/Saturation. There's a box in the corner that's labeled "colorize." Check it. It'll let you basically color an entire image thints and shades (COLOR THEORY) of one color. Since your lines are all black anyway, you can easily make the lines one color. Up the lightness slightly, up the saturation, adjust the hue last and you've got instantly colored lines.