We don't have a scanning guide here yet, as far as I know. I can share what works for me, but perhaps others who have scanned hand-drawn work can give some advice?

I set my scanner to 600 dpi, 16-bit grayscale (when I can. My home scanner only works at 8-bit, but the ones at school can do 16). I apply a 2 pixel Gaussian blur to the result, then scale down 50%. That usually smooths out the irregularities of the paper and graphite, giving me a 300 dpi image at the original physical size. If it's still too rough, I might rescan at 1200 dpi, blur by 4 pixels and reduce to 25%, but that scan takes a long time.

The resulting image goes at the top of my layer stack set to the multiply blend mode, so that the white will vanish, leaving whatever colors I paint underneath. I use this technique rather than trying to delete the white because it makes for nicer lines, without that light gray halo you get from the blend between graphite and paper.

From there, you can use the magic wand to select inside the lines on your top layer. Sometimes it's a good idea to expand your selection by a pixel or two to get it fully beneath the lines, but it depends on the drawing and the size you're working at.

This method works quite nicely for lines on tracing paper, too, by the way.