The paint bucket fills an area of something, in that something's layer. Whether it's a surrounded with lines area, or an existing filled in colored shape. It doesn't fill the same area of a different layer.
If you had a reason to need the colored areas to be in a different layer, you could duplicate the lines into the layer behind, fill in the colors, and delete the duplicate lines.
One worry about coloring in on the lines layer is that if you are doing some of that with the paint brush tool, the color may go over the lines. But, with the brush tool you can choose to have the color shape area go behind the lines. See this option that appears when you're on the brush tool.
