On the main body of the bushing, there is both an external thermocouple as well as a thermocouple that is integral to the heater. Which thermocouple am I supposed to use?

For the head zone, use the thermocouple that is integral to the heater. For the main body heater, it is recommended to use the external thermocouple, and only use the thermocouple which is integral to the main body heater, as a back-up should the external thermocouple fail.