The floppy disk needs to be formatted with the DOS Format command (in Windows 9x: FORMAT A: /S) and also contain a config.sys and autoexec.bat file.
The config.sys file typically contains the instructions to load your DOS CD/DVD-ROM driver while the autoexec.bat file contains the instructions to load Microsoft’s DOS CD-ROM Extensions (i.e. mscdex.exe).
Please consult your system’s documentation for the proper way to load your DOS CD/DVD-ROM driver and mscdex.exe. You should test this configuration with your bootable floppy disk before you make a bootable disc. If your target system boots properly with the floppy disk, and assigns a drive letter for the CD/DVD-ROM drive on that system, you are ready to make a bootable disc.
1. Start a new WinOnCD data project.
2. Click Bootable Disc Properties in the Project Toolbar.
3. In the Bootable Disc tab, select Create a bootable disc using data from partition and choose A: for a bootable floppy.
4. When you are ready to record, click the Record tab in the Project Toolbar.
You'll see no files on that floppy in WinOnCD - that's normal. Data will be transfered from the floppy and recorded to the bootable section of the CD...
I strongly suggest you try this on CDRW disc first to make sure the procedure is working.