The other image might be a waste of your time then. It will only automatically boot from the SD card on a reboot. A power cycle will require you to push the Boot switch button on the Beaglebone.

If you're powering down the S2, plug a wall wart or USB power supply into the Beaglebone to keep it alive while you do whatever requires the power down. Once you've applied power to the S2, remove the 5V power from the Beaglebone as it will pull power from the S2 IO board at this point.

The reboots from the SD card save the settings right?