Learning color theory and application advice (Digital art)

Have you watched the Color Course here at CGCookie?  I also completely recommend Gurney’s book.  Even though it says it’s for the realist painter, it’s completely applicable to digital works.  You may not want to go for anything realistic, either, but it’s important to understand how light and color interact in a realistic way to add more believability to your work.  For applying color to lineart, I would separate them out into layers.  Lineart on one layer, colors for various things on others.  If your lineart is drawn on a white background, you can use the Multiply blend type to only get the black lines and the colors will show underneath.  Good luck!