Hi Tim,
Don't know if this will help any as I use a canon scanner, but when I'm scanning pencil drawings, rather than scanning as a colour image I set it to monochrome or line art. I can also tinker with the brightness contrast settings in the preview till just right.
Another problem with pencil is you can sometimes get a reflection back from the graphite on the paper and what is a dark line then comes out white.
This may sound stupid but as long as your drawing is finshed, put some talcum powder on it and then blow it all off. There should be enough on the picture so as not to be seen, but enough to stop light reflecting back when scanning.
I too use PSP (V.9) and prefer to save as Jpeg. Preferable format for the web and is of decent enough quality to print also. If its better quality you are going for save as an EPS or PSD.
hope this helps