If you have Win98SE already up and running, you can make a bootable floppy via Explorer. Format the floppy, and make sure that you have "Copy system files" checked. Depending on your case, you may be able to just copy the system files without actually formatting.
If you want something a little more elaborate, I beleive there is a 'makeboot' script in your \Windows\Command folder.
If all else fails, Add\Remove in the Control Panel and click on the Startup Disk tab.
-SUO