I've got a new PC-98 game (Might and Magic: Clouds of Xeen) that needs both a floppy disk and a CD to work (the floppy contains the main executable, while the CD has the data file and the audio tracks). So I'm wondering... what do I do with this? Do I just add the CD to the database and put something in the comments field?
That seems reasonable. Might I suggest you see if you can send the floppy to the Software Preservation Society so that they can make a IPF of the floppy then its completely preserved. http://www.softpres.org/home
Off topic: looking forward to the release of KryoFlux.
Don't worry, I've already worked with them a few times. 
In this case, though... I think the disk is slightly modified (the game stores the configuration file in the same disk), so it wouldn't be up to the SPS standards. And in any case I can't make a SPS-style dump of a high density disk with my regular Amiga drives, so I'll have to wait for the KryoFlux.
In the meantime I will just create a regular image. It's better than nothing.