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1) Adjust the levels on the scan(Image>Adjustments) to kind of 'clean' the picture up; ie. make the blacks blacker and the whites whiter so the lines show up better

2) Select>Color Range to get all your black ink lines selected, adjust as necessary. You can also select the white and then go to Select>Inverse to get the same effect

3) Once all your lines are selected, make sure your Paths Window is showing. At the bottom of the paths window box, there are little buttons that will say "convert selection to path", "stroke/fill selection", and vice-versa.

4) Click on "convert selection to path", then you can tinker with the paths or go ahead and fill them with whatever color, usually black, you want. You'll probably want to delete the paths themselves after the color fill, and if you haven't already, delete the white spaces.

5)Use layers! Make sure to give the lines their own layer and lock it so you can't accidentally mess them up. There are lots of ways to color digitally, depending on the style and your tools. You can also make a separate layer for each color, for each section, or however you want, but always keep an untouched line layer on top. Remember to Flatten Image once you're done.