For this particular tutorial, I'll be using Valentine Val as an example image.

On my Layers Tab you will see how I arrange my line art and flats. Start by creating a layer below the line-art and label it whatever you want. For this tutorial I labeled mine Flats. Make sure that your line-art layer is set to Multiply.

This is a personal querk of mine that my line art is set on Grayscale, mainly because it is easier for my system to process, plus I don't need to worry about colors until later.