I wouldn't set it up that way. I fly with a pair of 730 mAh LiPo packs, each with my own design failsafe 5A programmable regulator set to the exact same voltage output. They share the load and the batteries drain down in a balanced way. If either side has a failure, the other side has the capacity to completely handle all the load that can be thrown at it.

Some seem to like the idea of having a "standby" battery instead of an active, redundant supply as I use. Ask yourself this question: How do you know the standby is ready to work if needed? If you use it every flight in an active mode, you can track the voltage drop after each flight and compare it to the other. If you never use it, you don't know what it can be expected to do the next flight.

Here's one real world example of why this can make or break your airplane. I recently bought 4 Thunder Power 730 LiPo packs, 2 per model. I was putting the 2nd set together for my backup Prestige, doing my normal bench testing of components, and saw a complete drop out of voltage from my regulator. New battery and a new regulator I had just built. I suspected my own regulator, just in case I had an assembly error of some type. Quickly did the troubleshooting to find it was the new TP battery with a bad crimp inside its connector, undetectable from outward appearances. It was an intermittent that had to have the wire held at a specific angle to cause it to fail. It happened on the bench test because I moved things around in between tests. Yet, you could static test this all day long and get perfect results, as long as you didn't arrange the wiring harness that specific way. In flight, with things moving from G's and vibration, it would almost certainly have failed. Had this been used as a "standby" that was adjusted to only work if the primary died, I might never know it had a problem waiting to bite me.