Hey! I remember my A500 DataFlyer controller. :-)
In addition to the things noted above, one special item to note is that the DataFlyer doesn't implement auto-booting in exactly the standard RDB way. The setup copies a couple files to the drive, and if you re-org or disconnect the drive that contains those files, you'll lose the ability to auto-boot until you re-run your DataFlyer utility. I never ran mine with more than one HD, but it MAY be possible that the auto-boot data files are getting written to the drive you're disconnecting. I seem to recall hearing that happen, before. (So, really, your external drive could act as "boot" and then turn over control to the highest-boot pri partition. Of course, if you disconnected your external, the system wouldn't have the needed files, and would sit and wait for a boot disk. These symptoms also fit your problem.)
As for your other questions -- Yes. You should boot only from the DataFlyer floppy disk when making changes to a drive connected to the DataFlyer. Otherwise severe data corruption in the auto-boot code written to the hard drive could occur.
I think the hang-on-CDROM-detected was fixed in a newer version of the DataFlyer software. You can use any DataFlyer Prep driver disks that have A500/2000 SCSI support. (including the newer IDE/SCSI dual cards) Maybe you might want to scour the web for a newer version?
