I run Win98SE and for historical reasons have a SCSI as boot drive C: I added a large IDE some time ago without trouble.
I think you may find the answer in BIOS. I have it seeking SCSI as boot drive and allow the computer to call my IDE the primary master.
It simply works that way, the IDE is jumpered to master as well, and is connected to the Primary IDE socket. The important thing seems to be to tell the computer to seek the SCSI for booting purposes.
All this assumes that your computer booted from the SCSI before you added the new HD.