I think the 'conventional' way is the one you have marked as 'Possible' - that is your Arduino is powered via the USB port but the rest of the system is self powered.
When you implement the solution you then have to bring back a 5v supply to the 5v socket on the Arduino board.
You could also program the Arduino to check the 5v via an analog port and alert you when things were not right. A simple flashing LED would suffice, probably.