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It's been a long time since I last did things this way, I hope I can remember it all correctly.
The first thing you'll need to do is ink the image. You can get away with pencil if your lines are very clean but it's not recommended. Ink is easier. The less tooth the paper has the better it will scan so don't use normal sketchbook paper, use something very smooth like printer paper. Scan the image and adjust the levels so that the image is clear and the paper is as pure a white as you can get. My explanations will all be using terms for how they're called in Photoshop but there should be equivalents in other art programs.
Way 1:
Go into channels and use them as a mask to make a selection. Invert the selection, then on a new layer fill the selection with black.
I couldn't figure out how to do this in Krita but in there you just have to tell it to convert the layer to a selection mask.
Way 2:
Set the layer to multiply. Color on a layer underneath. This has some disadvantages but is the quickest method.
Way 3:
Adjust the levels so that there is only black and white. Delete the white. This only works when the original image is scanned at a higher resolution than you want the end result to be and doesn't work well if the lines are scratchy.
