Yes. We recommend using fully charged batteries for performance reasons only—so that people get the best possible experience with the Launch Box, particularly on their first try or when they are just learning how to use it. There are no problems with using partially charged batteries, as long as there is enough charge for them to be usable/useful.
There is also no issue with pulling a battery from the charger and using it before it has been fully charged (again as long as enough charger is useful). However, it is recommended that you let the charger complete its charge cycle whenever possible as the microprocessor in the charger may attempt to implement a conditioning cycle on the batteries. If it senses that the battery is low, it may discharge the battery before recharging it so as to extend the battery life. The charger that is being shipped is a smart charger and is designed to make the batteries last as long as possible.
The one thing that it IS necessary to watch for is putting an already fully charged battery back into the charger. Due to the nature of how the charger works, it is likely that the charger will be unable to determine that the battery is already fully charged, and will attempt to charge it again. This can potentially cause overheating in the battery and battery damage.