Hello pollon,
I first recommend that you first don't think about the actual coding, but rather just plan out what you want the application to do. Will both fans respond in the same manner? What type of control loop do you want to have? How fast does your control system need to react? Who will be the end user of the system? Does the setpoint need to be adjustable? What about the control algorithm parameters?
After you have answered most of those questions and any others that come up in regards to the desgin requirements, you should then define the requirements for your hardware interface. Do you know what type of thermocouple you have? Have you considered using multiple thermocouples to get a better idea of the temperature in a larger volume? How do your fans need to be controlled, PWM, Analog Level, digital commands, etc? Any compelling reason that you are using two fans?
After those additional questions have been answered, I recommend that you search ni.com and google for some of the following terms: temperature, control, loop, fan, PID theory, etc.
A search for "temperature fan control" yielded
NI Ready-to-Run Controls Starter Kit as the second search result.
Good luck with your project,
NathanT