Rather an old thread now but thought it worth adding my experience for the benefit of others who find this thread by search, as I just did. The penny has only just dropped for me about how to use these things.
I have both Original Juice Pack (1800mAh) and Juice Pack Air (1200mAh). (The phone is 1200mAh)
I did several experiments where I connected a full juice pack to a fully discharged iPhone 3Gs. I was expecting the Air to just recharge the phone to 100%, and the Original to do it with one or two blue stars still lit on the back. In practice the Air will take the iPhone up to 60% and the Original to 100%, at which point the Juice Packs are fully discharged.
As this thread implies, and the Mophie site states (but I didn't understand the implication when I first read it), the process of transferring charge from the Juice Pack to the iPhone is only about 60% efficient. ie you lose about 40% of the capacity of the JuicePack by using them as chargers.
Much better (as stated in this thread) to charge the Juice Pack and phone fully, let the phone use up the Juice Pack's battery before it uses it's own. That way you get to use the full combined capacity of the iPhone and Juice Pack, 1200+1200=2400 for the Air, or 1200+1800=3000 for the Original.
If you use the Juice pack as a charger (ie only switch on the Air or plug in the Original when phone is flat), you will only get 1200+0.6x1200=1920 from the Air, or 1200+0.6x1800=2280 from the Original.