you whernt planning on starting it with one battery, taking it out of the car while it was still running and put the other one back were you? if you did that the moment you took the battery out wile it was running, the alternator would blow up because the engine is demanding too much power and the alternator cant handle it. and if the battery was stuffed it wont charge and sraw all the power out of the alternator and the engine will just die.