No problem using extra battery packs. You do not lose your transmitter settings. On planes where the RX battery is difficult to replace, the field charger is handy. Many systems allow for about 90 minutes of flight time. For example, I have found that a 600 mAh receiver pack will run at least 90 minutes of flight time on a 4 servo sport plane.
Next time after you fly for only one hour, when you get home, run down the packs on a cycler. I bet you still have a lot of capacity left. If you do not have a cycler, this is more difficult to determine, but you can sit in front of the TV and work the sticks back and forth to simulate flying conditions.