Thanks to Jason Marchesano our local UCS systems engineer for providing the answer to this issue. There is no need to back up the configuration if the intent is to persist the state of the configuration in the VM across reboots. There is a radio button under the browser-based portion of the UCS Control Panel:
Open your browser to the UCSM IP Address
Click on Emulator Settings on the Bottom Left
Choose Database Persistence -> Preserve UCS Database upon Restart
Restart the VM with DB reset to initialize the settings.
This is all correct. We are working for a future release to support taking a backup from a live UCSM into the emulator and vice versa so you can grab your entire config from a live system and import it (equipment, config, and all), as well as supporting the ability to take a XML backup from the emulator and import it back into a live system (configuration only). This coupled with adding the needed emulation to make backups in the UCSM GUI should also achieve a even richer experience with UCSPE.