If there is no OS on your "spare" drive, mount it in the spare bay and fit power from unused lead.
Fit a data cable to the Secondary place on the mother board and that's it. (Or so you can hope)
If there is an OS on the "new" HD, and assume there is no data you need on it, then it is much safer to disconnect temporarily the Primary HD data cable, boot from your 98 setup floppy and at the A:> prompt run the FDISK routine. Or if there are no partitions, FORMAT - to clear this secondary drive of everything.
If you have done all this then shut down again, reconnect the Primary drive and reboot as normal.