Greetings,
This is definitely possible with NI-DAQmx, but not with the DAQ Assistant. The example Acq CJC Temperature.vi demonstrates how this is accomplished. This example is available in the following location:
Hardware Input and Output >> DAQmx >> Analog Measurements >> Temperature
The example only acquires a single reading, but you could easily modify it to continuously acquire and chart the CJC temperature.
Good luck with your application.
Spencer S.