I don't think so as Win98SE has support for large drives. Of course, I never give more than 10 gigs to Windows, myself as I need it for real work in Linux.
The first step is knowing exactly what your partitioning is (Microsoft can do wierd things).
If you can boot to a linux prompt, post the output of this command and I can give better instructions. I recommend having a few linux "live" CDs (runs from the CD) handy so you can easily tell how your system is setup.
That should return a list of all your hard drive partitions.
# Cheap CDs
Discount Linux CDs