Melissa -
The drive should be detected at the DOS level without any special drivers. Before you try to load Win98, try to boot with a regular DOS diskette (a 98SE if you have one) and see if the drive can be seen and has a letter assigned. If not, you need to FDISK (partition) it again and format it with the /SYS switch (assuming you're planning to boot from this disk). I realize you already did this with the utility - no idea why that didn't work. But if you can't even see the drive with Win98's FDISK command, then there's something wrong with the motherboard recognizing the controller card to begin with.
If you're already at this point (FDISK can't 'see' the drive), then you might look at other BIOS settings to see if the controller's PCI slot is disabled - or just move the board to another PCI slot to see if it helps. You should also try the BIOS 'reset configuration settings' option and then clear your CMOS setup, especially if you try moving the board to another slot.
Your goal, before attempting the Win98 install, is to get the DOS FDISK to see the drive. If it can't, the install will never work. If you get FDISK to work, your next 'goal' is to get the drive formatted with the /SYS option and get the motherboard to boot to a generic C: prompt from that disk.
The only thing to set on the motherboard BIOS for the booting part is an option to boot from a PCI SCSI device (labeled a BOOTABLE SCSI or BOOTABLE IDE DEVICE or something like that). This has nothing to do with DOS or 98 recognizing the drive letter - it only tells the motherboard to check for this device during the boot process. In addition, there should be an option to change the order that boot devices are checked. You should be able to leave the old drive in and simply move the 'Bootable SCSI device' ahead of it in the boot order.
There *is* a Win98 driver for this board - it only helps with performance in Win98 and it has nothing to do with your current install problem. Don't worry about installing/updating the driver until after 98 itself is installed.