Do you know the reason for the low battery? If you disconnected the battery, you may have to reprogram the battery, but I think only new batteries need to be re-programed. The alternator will only operate whe the engine is running as it is connected to a belt driven by the running motor. It stops turning after the engine is turned off. Like Mark above stated, the fan from the radiator may still be running. Lift the hood and look, and listen. If the battery goes down again, have the battery tested for a possible bad cell. Do you have air shocks? It may be adjusting the car to a level position after you stop or charging the system. Some cars have that suspension system and the air compressor will charge the tank up even if the car is turned off.