Thermocouple amplification configuration
Your signal conditioner contains linearization and automatic cold-junction compensation, as well as isolation. If there's an option to turn it off, don't do that. You'd only want to turn it off if you were doing some kind of strange differential measurement with two thermocouples. 

All you have to do to get degrees C from the output voltage is to scale and offset the resulting value to represent the temperature range, which apparently is configured via a software interface with the signal conditioner.