I have a large collection of physical software install disks. I've purchased a Floppy EMU. What is the best way to get my disk collection onto the Floppy EMU?

If you are talking about making disk image backups of application programs (not your personal data), then I would recommend you first check if your disks contain software not already on the Macintosh Garden. I don't just mean the title, but also the version. If the same title and version appear on the Garden, then there would be no meaning for you to take time to convert a real disk to an image. That's the way I go about it regarding my own floppy disk collection. But if you have a different version than what is on the Garden, it makes sense to image the floppy (and hopefully you can upload it to the Garden).

If you don't mind using System 7.1.1 and newer, ShrinkWrap 3.x is create for creating images from real floppy disks.