What I do is after I create the lines to a character (yes, I mostly do characters), I expand the lines. Then put everything into one group and then duplicate the group. I then keep the top group as a safety and lock it (I also usualy name this layer line art). Then the bottom group... I create Live Paint. Usually I turn off all the colors while selected. I then click off. Select the Live Paint fill tool and choose a color. Then I fill in the areas.