Maximising Battery Life - 9v 1200mAh Lithium powering a 5v Heatpad

Do you need it to run full time to keep above your minimum temp?

If the heating pad provides a 40 degree differential over ambient, when you are only a few degrees below your min temp, you could use PWM with a very low duty cycle to save power. Then, when it gets colder, your duty cycle will go up.