Cheers mike, you're a star.
I'll try it both ways, see which works best.
Any recommendations on specific parts? I've found a quad op-amp IC that looks suitable but I'm not aware of any unknown unknowns that I should be avoiding.
I was only planning on being able to differentiate between a few different colours of marker pen, so low resolution might be fine but then again, different makes/brands/shades of markers of the same colour might throw a low res sensor off.