I still have never figured out how to get a save file onto an emulator. I figured out how to get the code off of the hardware (I photographed it all), but when trying to load it within Magic Engine, there didn't seem to be a way to enter in the code.
You enter the code on your PC by executing pcetohd.exe (You do
not enter the code within the nanami bank software itself), then the actual game save file is
replicated on your PC. Then when you feel like restoring those save file(s) to the actual hardware, you link these save files onto an iso, then either burn onto actual CD-R (for actual hardware) or mount the image using Daemon tools (for emulators). You can then "restore" these save files to actual hardware/emulator with nanami bank's restore option.
I use ootake, but I did do a Magic Engine -> Actual Hardware transfer once (so I know vice-versa can also be done), but it's definitely a bit of a hassle -- well, this whole procedure is, but there's no other foolproof way of backing up your save data to a computer as far as I know.
What I do recall having to do for Magic Engine was having to fiddle around some setting so that each game would have its own "save bank", as opposed to all games sharing one save bank.
Once that's done, you start up nanami bank, then that will create its own save bank save data as well (that is, magic engine thinks that the nanami bank CD-R is another game, so it will dedicate another entire save bank just for nanami bank). At this point, you "restore" the individual game save file to the nanami bank "save bank". Now, you just rename the nanami bank save bank data to the game's save bank data, at which point you'll be able to boot up the game.
Going the other way (emulator -> actual hardware) is slightly less of a hassle, as you can simply crop out the actual save game portion of the data using a hex editor on the save bank data, at which point you can simply rename this file for your backup, or get ready to restore tbat file using hdtopce.exe app.