Under Layer 1, where the drawing is, I create a new layer to work as background, and with the paint bucket, I colour it light blue.
Then, I create another layer, which will be the layer where the base colours will go, the flat colours. I will start with the skin colour.
Summary: in the layers window I have, first, the layer with the transparent picture and black lines. Underneath this layer, I have the layer which I'm colouring and finally, I have the background layer, in a uniform light blue colour.