People keep asking how I colour, so here's my process for a typical page:

1. Scan inks at 600dpi, bitmap mode, clean up, then convert to greyscale and then RGB.
2. Put the lineart layer on top, set to Multiply.
3. Flats: a new layer under the lines. Magic wand with anti-alias OFF on the lineart, fill each area with a flat colour. Every object gets its own colour, even if it'll end up the same.
4. Lock transparency on the flats layer, then shade on a layer above with a hard brush, layer set to Multiply.
5. Lighting on another layer set to Screen or Overlay.
6. Flatten a copy, resize to 900 pixels wide, Save for Web as JPG around quality 70.
   

The flats step is boring but it makes everything after it ten times faster.

Thank you SO much for this. The anti-alias off thing is what I was doing wrong.

Stickying this in my brain. Also bookmarking.

Pro tip: record the flats cleanup as an Action and bind it to an F-key.

this helped so much. what do you do about gaps in the lineart, the fill goes everywhere

Close the gaps on a separate layer with a 1px pencil before you fill, then delete that layer. Or just fix them in the inks, it's good practice!