Bernie will only boot from a disk that is 32 Mb or less. It can be a disk image created by Bernie or Disk Copy, but even cooler, if you have enough memory, is to create a RAM disk that is 32 MB or less from the Memory Control Panel. check on the "Save to disk on Startup and Shutdown" option. Then format the RAM disk to Prodos. Now you can copy your main setup to the RAM disk.
Your RAM disk can now be used to boot Bernie. Even when you shutdown the computer and restart, the Prodos files are still on the RAM disk.
Another option is to set up the function keys on your Mac. I have mine set up that when I press F1, Bernie starts up and boots into my main boot disk image.
Even cooler yet. Make a duplicate of the Bernie2theRescue folder. You can have two or more windows of Bernie running at the same time, each booted into a different startup disk. You can have one Bernie booted into DOS 3.3 and the other Bernie booted into Prodos.