sounds like maybe you are over proped, what size prop are you swinging, that would be one reason why your motor is smoking, and short flight time, try runing a smaller prop, also what voltage is the motor rated at, the speed controller really has nothing to do with the run time, or motor burning,

also if you are over proped the motor will draw alot of current, and with small batteries if you draw too much current the batt voltage would drop dramatically, therefore the speed controller will shut of... i hope this helps