If your internal drive is your boot drive, then turn off the autoboot on the WordSync2000, as your not booting from that card, only using it as a secondary SCSI device. The install disk should only seeks hard drives attached to that card, and list them accordingly.
In this scenerio, those drives would not have boot partitions when you set partitions. Look at the list of drives, and your internal drive should NOT be listed as available.
BTW, that card is Zorro-II and only SCSI-1.