I regularly use Tahoma2D and in the one of the nightly builds there is the option to set the fill tool to “refer visible”.
This means that when you have two layers, a layer that contains the lines and under that a layer where you do the painting in , you can use the fill tool to fill closed shapes the exits in the lines layer.
This is what I used when I imported the drawings from Animation Paper into Tahoma2D for coloring.
Bert