It's much simpler than that. Since you already reformatted the drive, I understand there is no important data there.
You'll either need a bootfloppy or Windows 98 SE bootable CD.
Boot into command line (in case of the Win98SE CD it will be "boot with CD-Rom support" or something like that) and run fdisk.
On the Win98SE CD it's located in Win98 subdirectory IIRC, so you'll have to change to the CD drive letter first (by typing in it's letter, in your case most likely D:), then enter that directory by typing cd Win98 and then run fdisk.
If you've booted from a floppy, you can run fdisk right away.
The program should be more-or less self-explanatory, but if you have any questions feel free to ask.
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"God. Can't you people see I'm trying to commit a crime against science and nature here?"
-- Reed Richards
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