It's been a while since I've had involvement with Netware configuration, but I've recently had to add a tape drive to a Novell Netware 6.5 SP6 server - the key point is to update STARTUP.NCF on the DOS partition to include the required drivers for the SCSI card. For example, I added the lines:

LOAD NWTAPE.CDM
LOAD LSIMPTNW.HAM SLOT=2

The PCI card is loaded into PCI Slot 2 (hence the line above) - you can check which slot your device has been installed to by checking Novell Remote Manager (http://yourserver:8008/ or https://yourserver:8009/), under 'Manage Hardware' -> 'PCI Devices'. Once the driver has loaded (you can load the above drivers manually, without having to reboot the server), check the device is visible using 'LIST DEVICES' on the console.