If you have a layer below the layer with the lines, you can use the brush tool to color in stuff
Or the way i do it is i use the magic wand tool with 0 tolerance and i select the outline (i usually have it set to 3 pixels), once it's selected, i invert the selection (Ctrl + I) and on a layer below the one with the line, i use the paint bucket and fill in the area inside the line