Sandorski,
Win 98 is NOT Win NT friendly, it will completly whip out your MBR. Go ahead and install Win 98, but make sure you have a boot disk for NT (or a bootable CD). Re-enter WinNT setup, and do a repair installation, only choosing to rewrite the master boot record.
Also, remember that Win NT (if its any version before 2000) will not be able to use Fat 32, so you may want to use Fat16s. Hope this helps.
Cherny