win 98 has a fat32 fs.
check out http://www.gnu.org/software/parted/parted.html
i think there are also some gui's to resize partitions (partion magic, etc.) but some are commercial and so forth.
gnu parted is not that hard, but one must read up on it and how to use it - most likely you will end up formatting your disk if you dont research before hand.
also, before the resize make sure you make a backup of all important data - since such procedures are not completely safe. to decrease the chance of data loss run a defrag on windows before re-partitioning.