Hello,
There should be no problem running 2 PID loops at once. However, depending on your hardware, you might be limited by the rates that your PID loops will get data.
For example, if you are using an E-series board, you will have to acquire all your data for both PID loops at the same rate. The PID loops themselves could be running at different rates but, the data acquisition rate has to be the same because there is only 1 analog to digital converter on E-series boards.
If all your inputs to both PID loops can be done at the same rate, then you are good to go!
Nicholas C
National Instruments
Applications Engineering