This illustrates the most common process I use when colouring ink and pencil drawings, when I'm not aiming for some innovation.

(1) This is the drawing, scanned in at 600DPI in colour and adjusted with Levels for a rougher look. I usually scan it in several colour-corrected modes and grayscale, and then select the one with a good balance of light and dark that serves the effect I want to get. Despite being a grayscale picture, I sometimes like scanning it in colour because of "incidental" hues that turn up when I work on it later. Also, with these kinds of drawings, I tend to put the shading and texturing in the pencilwork.

(2) Here I spent about an hour filling in colour blocks with an aliased (non-blurred) brush or aliased selection tools, working them from perceived "top" to "bottom" layers. I tend to tweak colours and levels locally a lot, and having these "masking blocks" helps muchly.

(3) I create a new layer, and using Magic Wand at 0 Tolerance, I select and fill up the blocks with colours generally close to what I intend. Most of the work is in tweaking the blocks with Hue/Saturation for the best colours. I also mess around with different Layer blending modes. In this case, the Burn modes ended up too strong over the dark pencils no matter what colour I used, so I went back to Multiply.

(4) Put some finishing touches on it, and further colour adjustments. The eye is done on a separate layer for glowy effect. The fire is done by taking a photo of a flame and reducing it to only 4 colours using Levels. A layer mask was used to merge it with the drawing.