Yeah the whole back up battery thing won't fly.
If you really want to get into Brown Out Prevention
1)
Load Test your batteries. I recommend sharing this with your alliance partners at competition.
2) If you want to get more advanced: Have your code monitor the power usage on the PDP and reduce power to motors accordingly:
http://www.ctr-electronics.com/contr...ical_resources
3) You can prevent it by design if you do some analysis for your power consumption and set a power budget. There has been discussion on various threads here in the past about that.
Depending on your design I would add the ability to control power on your motors on the driver station and allow the drivers to override/control power as necessary.