Instead of generating 2 different signals you can make use of the relay's NO & NC contacts for heater and cooler.The advantage is that at any point of time only on of the device is turned on.It doesn't require monitoring whether one of the devices is turned off while the other is working.
I think that Jure is better off with two independent channels - I have written PID and PWM codes in LabVIEW (Jure: email me and I can send you LabVIEW 8.0 codes) but there are times when one wants to be neither warming nor cooling.
So having a logical NOT on one channel to drive the other is not a good idea.
Thanks for your answers. James i send you message with better explanation of the problem, but you are right, there are times when one wants to be neither warming nor cooling. My other problem is to connect PID with PWM.