In Classic Mac OS (up through 9.2.2) every disk has a desktop folder. Every disk that is mounted has its desktop folder displayed.
As such, if you have, say, a Mac SE/30 and it's booting system 7.1 off a hard disk. When you create a file called Letter to Granny (in SimpleText, for example) and put it on the desktop, it's going to the desktop of your boot volume. It's being stored at
Macintosh HD
esktop:Letter to Granny
If you have a boot volume and a second volume (a floppy diskette, for example), when you save onto the desktop, it goes to the desktop of the boot volume, still at
Macintosh HD
esktop:Letter to Granny
However, what should happen is that you can move the file onto the diskette so that it's at
Corys Data Diskette:Letter to Granny, and then from there, I think you can move the file onto the diskette's desktop folder, so that it displays on the desktop but when you put away or eject the diskette, the file disappears off the desktop. At this point, it would be on
Corys Data Diskette
esktop:Letter to Granny
If you're installing your operating systems onto different partitions or physical disks, then ejecting them when you're not using them should help, but you'll likely still get icon interference right when you boot up.
Also to my knowledge this doesn't work on network shares, but I'm putting it on my to-do list to check this out on my 180 or 6100 to confirm what I think is happening anyway.
Mac OS X changed this behavior, of course, by being a BSD userland and a mach kernel, so in OS X land, your desktop is of course at
/users/$USERNAME/desktop rather than just at
/desktop (or really,
Macintosh HD
esktop:)