How big is your hard drive? How much space do you want/need to allocate to each OS?
Those are your first questions. Once you decide that, SAVE ANY CRITICAL LINUX DATA YOU MAY HAVE, then use the fdisk that came with Linux, not Windows or DOS, to set up the appropriate partitions. I would allocate Win98/FAT32 to the first primary partition (bootable) on the drive, then set up the appropriate extended partitions as Linux (native or ext3 or reiserfs and swap).
Then use Win98 and format the Windows partition, install Win 98, then install Linux (it will format your Linux partitions), and install Lilo or Grub in the hard drive MBR.
Someone else may have a better idea, but that should be pretty much it.