I use two battery packs run through two separate regulators each going independently into the RX. To save weight I have a primary and secondary battery. The secondary is as small and light as I can find and uses a 5.4 or 5.1 volt regulator. The primary battery is on a 5.8-volt regulator. What this does is cause all juice to be pulled from the primary battery UNLESS the primary battery drops below the voltage of the secondary regulator. This means that the backup battery never comes into play unless needed and therefore only has to be big enough to last one flight (this assumes you check the primary prior to each flight).

I previously use a 5-cell AAA 750 mah battery as my backup (to keep the weight down), but now that I've gone lithium here's my setup:

Primary: Lithium Ion 2000 mah (3.4 oz) on a 5.8-volt regulator/switch (1.? oz).
Backup: Lithium Poly 900 mah (0.4 oz) on a 5.1-volt regulator (1 oz.)

I've probably put 50 flights on the plane since last charging the backup battery and it's still at max charge. That's because no current is every pulled from the backup because the primary lithium Ion never drops that low. However, if my primary every goes out (again) I can fly for about an hour and a half on the backup! To me that's well worth the 1.4 oz penalty!!!

Another nice thing about this setup is that the regulators (Oddino's) won't allow ANY reverse flow in case one pack goes out. I've discussed this with Jim Oddino and tested it myself.