Well, one of the solutions is after you scan the pictures to send them to one of your art programs (paint, paintshop, photoshop, ACDSee, etc.) and choose the automatic contrast tab that most of them have. It will automatically darken the lines and make the pictures visibly more clear and defined.
Most of the time, people don't draw heavy enough lines, and so its a problem from the start, when they draw. If this is the problem, once you've outlined your pictures it would help make them look better to darken the lines or ink them. If you do that, the scanner, provided its of good quality, should not have a problem scanning in the quality. I've never had this problem with my work because I darken my own lines or ink my pictures. So if you aren't already doing this, I suggest you do.
As I've never heard of the brand "Visioneer", and as a I have an HP (Hewlet Packert) scanner, I'm not sure how you would convert files in the scanner itself. You can always do it in the afforementioned art programs.
Hope this helps.