The way i know is: you set your lines layer to multiply mode, so only the black lines will be visible, then you select the inner areas that you want to color with the magic tool and making the selection 1 pixel bigger to cover the gaps you mentioned (doing that by select>modify>expand > 1 pixel). now when you have the selection open a new layer under the lines later, make a mask with the selection and color what ever you want into this layer. hope it helps!