First, start out with your scanned grayscale art that is already anti-aliased. If it is grey or uneven, adjust the levels (Image>Adjust>Levels or Crtl+L) to make the whites white and the blacks black. This might take some trial and error to get right, but usually, there will be "spikes" that indicate where you need to move the arrows.
Next, select all (ctrl+a) and copy. Create a new layer, go to Quickmask mode (hit the q key), paste, exit Quickmask mode (q again), and invert the selection (ctrl+shift+I).
With black as your foreground color (to make sure, hit the d key, which sets your foreground color to black and your background to white), fill the selection (ctrl+del or backspace).
You will end up with your linework seperated out, with transparent anti-aliasing instread of greyscale.
It is a good idea to lock the transparency of this layer now, so even if you accidentally color this layer, you can simply fill with back to restore it. This also allows you to color you line work if desired.
Now, create a new layer under your line art layer and apply your color to it without changing your original line art.
I usually create a background color layer to show any areas I have missed with character color (ie, eye highlight, which may look fine with the checker board behind it, but will fill with green when the background shows through).
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