Here’s a quick how-to on colorizing lines. I don’t do this very often, but have on occasion, and it definitely softens the look of drawing. I drew this doodle in MyPaint with all my lines on a separate layer from the color flats, then saved them off as separate PNG files. Then I opened the bottom layer PNG in The Gimp and add the other PNG’s as layers on top of that.
Now the colorizing is done with the layer containing your lines, just click on that layer in the Layer dialogue and select Add Layer Mask, then “Transfer layer’s alpha channel.” (If your lines are not on a transparent layer, you should choose “Gray-scale copy of layer” and click the “Invert Mask” box.) Now you simply paint colors on your lines layer over your lines (no need to due a neat job, the layer mask takes care of that) normally selecting a darker shade of the flat colors below. Maybe I should just make a video, that was sort of confusing?