I fly my bigger choppers with two packs instead of one. (2x 4400 mAh 3S1P).

The only real drawback is that you need to charge twice as many batteries for a single flight. I've got 2 (er, actually, 3 now ) chargers, so it's not a big deal for me, but not everyone has multiple chargers.

You also get a nice mess of wires on your bird.
But it's nice to be able to use the same batteries on smaller models, so it's a good route to go if you want to save money.

Here's what the wiring connectors look like:

Parallel
http://www.truenorthernhobbies.com/p...roducts_id=116

Series
http://www.truenorthernhobbies.com/p...roducts_id=115

You would use two parallel harness' to connect the two sets of batteries to make them 4400 mAh, then use one series connector to connect the two parallel leads to increase their voltage.


EDIT: I forgot to mention that if you go the multi-pack route, it's important you have a balance charger on hand, since running different packs of different age will inevitably cause some difference in how one discharges compared to the other. It's a good rule to not cut it too close in terms of flight time or you risk draining one of your packs to low.