I've attempted using colored lines in the past, always with some glaringly tacky results. This time, I went about it differently. Instead of coloring the lines first, I did all of my lines in black on different layers (like hair, skin, ect), put down the flats, and adjusted the hue and saturation. For some lines, I had to continue adjusting the color as I put down the shading, because it clashed or just wasn't dark enough.
I realize I should start getting serious about backgrounds, because mine are pretty awful. That'll be something I'll be working on in the upcoming weeks.