Assuming you're talking about OS3.9, all I had to do to create an Emergency Boot floppy was make sure I was booting from a device on the FastATA and that the CD file system was loaded. I inserted the OS3.9 CD, clicked to create the Disk and just followed the prompts - when it said if I wanted to copy my IDE adapter setting I just said "Yes". I didn't have to manually fiddle with anything and the system just rebooted off the floppy with the CD inserted.
