You may find some dispersion in the charge state of some of the cells. When you are done, resume charging as before. All models need some form of throttle control. The simplest mechanism is a toggle switch on the side of the model which the pilot switches on physically at takeoff time. The model then flies until the battery is depleted, at which point the pilot lands the plane and flips the switch off.
Most fliers desire a little more control over their airplanes, however.
The next simplest mechanism is to have a mechanical or electrical switch in the plane that may be activated remotely. This allows the pilot to turn the motor off and on at will. For sailplanes and small models, this is usually sufficient. This device switches the motor on and off rapidly, with a switching duration dependent on the throttle setting. Thus, the pilot has a proportional throttle control analagous to gas-powered planes.