If you have adobe illustrator cs3 or higher there is an auto vector that traces it for you called Live trace.
When I do my art on the computer I use a graphics tablet, and create a new layer then ink on the new layer. When you have completed the inking delete the layer below it and you will have fresh transparent inks to color underneath.
If your pencils or inks are very clean you can scan then and merely darken them through brightness/contrast, select all, cut, paste in place (this brings it to a new layer) and then remove all the white by selecting the magic wand tool, untick the "contiguous" box at the top of the screen (this will make it so it selects ALL the white, not just one area) up the tolerance (top of screen again) to 140 and click on a white area, hit delete. You how have the lines only and its transparent to be able to color under (this is how I do most of my lines)
