Hello Arun,
By no means is this a stupid idea. There's a reason for everything, it's just a matter of understanding it. Just keep in mind that a temperature measurement is not all that complex and that the NI-DAQmx driver has been created and tested exhaustively to guarantee that the Thermocouple instance of the DAQmx Read.vi appropriatly compensates with the CJC specified and converts the voltage signal to appropriate temperature units.
If you are going to read the voltage from the thermocouple and the CJC on different channels, then I recommend using a VI called Convert Thermocouple Reading.vi. This VI may be found on the Function Palette >> NI Measurements >> Traditional NI-DAQ >> Signal Conditioning. This VI will allow you to gi
ve it a voltage waveform, specify the thermocouple type, CJC source and value, basically everything that the DAQmx task set to thermocouple would allow you to specify as well. You can also dig down into this VI to see the actual mathematical calculations that take place if you are unsure of it.
I'm not sure if by MAX being transperent to the user is what you want or not, but I'm going to also recommend that you do use MAX to configure your DAQmx channels and tasks. Once you have them created, you can actually test your settings in MAX such that you can determine whether or not the data you are getting is correct or not before you ever touch LabVIEW. If you have any questions on how to utilize your channels or tasks in LabVIEW, please let me know and I can assist.
Jared A