Yes, you cannot perform two DAQ processes with the same DAQ card at the same time. However...
If you acquire all of the data in your control loop, you can place the two channels into a buffer that the second loop can access at it's leisure. You can do this through local or global variables, but you will have to deal with the possibility of one loop accessing the variable while the other is in the middle of using (adding to or deleting from) the buffer. A "storage" VI with a while loop-shift register to store the buffered array would be better as only one occurance of the VI will execute at any one time.