I would roll with this:
1. Two A123 1100 MAH packs - Each could provide you enough flight time for maybe like 5-6 flights of about 10 mins. A typical 50cc sized plane will draw about 200 MAH per 10 min flight on an A123 pack.
2.
http://www.fromeco.org/Products/04FR...s/Default.aspx Get yourself a Badger switch with your dual battery switch and call it a day.
Remember the theory of your back up battery is that it should only come into play if your MAIN pack fails. This being so you could run a much smaller pack as your back up.
Honestly most 50cc planes can not handle much extra weight. The more complex systems you can add to them the more they will not fly great. Honestly the ONLY extra weight I would think worthwhile would be an additional RX battery. Still A123 would be a great way to go because with 6.6V you wont have to use regulators.
Myself I fly with servos that can handle up to 7.4V so this is a non issue. However being able to eliminate regulators is a nice thing. Once less thing to fail.