If it is a LiPo battery you must NEVER run them "completely down"" as this will ruin the battery or make it so that the charger will be unable to recharge the battery.

The LiPo chargers need to detect a certain voltage level before they will start a charge cycle.

If the level drops to say 2.0v per cell or less, the charger will NOT charge the battery as the battery is assumed to be ruined.

Bear this in mind if you are using LiPo's and make sure that you have the low voltage cutoff properly set.

Also remember that a 5 minute run time on the ground will probably translate to 8-10 minutes in the air, once the plane is unloaded ( but not at high throttle settings... ).