Hello;
In case you don't need to synchronize or correlate the Analog Input task with the Analog Output task, and if your two VIs won't access the same NI-DAQ functions on the same time,you can run 2 VIs independently.
Anyway, it's a better practice to compact both tasks in one single VI for maitenance purposes.
Hope this helps.
Filipe A.
Applications Engineer
National Instruments