Assuming you have a real (bootable) Win98 CD-ROM - just stuff it in there, and boot from it. The board supports booting from an El-torito CD-ROM image. You will have to set the BIOS to look at the CD-ROM first, of course.
Remember, with the latest version of the Intel BIOS, the dot.station becomes a regular old Intel based system. I haven't tried my retail Win98, but I know that Win2k and WinXP can both be installed directly from the CD-ROM. The floppy you have is basically a DOS disk with a bunch of CD-ROM drivers on it - for systems that predate the el-torito boot method, or that don't properly support it.
Oh, I forgot to note (thanks kludgemeister) that the board DOES supply 5V to the CD-ROM header. It is designed to go directly to a laptop style CD-ROM - and provides all the hooks. (I'm not sure about the audio - but I wouldn't be surprised if it was hooked up).
If you do use an adapter cable, you can actually run power from the adapter board to the CD-ROM board directly from the mainboard. In fact, that is how my system is setup. I have a ribbon cable, but you could use an adapter board, and simply replace the male Molex connector with a (longer) female floppy connector. (obtained from an old PSU if you have it). Then, you don't need additional splitters, etc.
If you can find the GCT/Allwell cable - it is even simpler. Just connect the 44-pin header to the mainboard connector (aligning towards the rear - leave the first 6-pins open), connect the standard 40-pin ATA cable into the CD-ROM adapter's ATA connector, and the 2-pin power cable into the power connector. You may have to trim the plastic on the power connector to get a good fit. (I actually replaced the 4-pin connector with a 2-pin connector, but trimming the plastic works just as well) It works great, and is a single cable solution. I spooled the excess cable into the metal cage under the CD-ROM.
-radarman
