Normally you will use a direct acting valve positioner. It has nothing to do with your controller except for the fact that you may have to change you controller action depending on which way your valve positioner is set up. The only time you want to use a reverse acting valve positioner is when you want to "reverse" the fail action of the valve. (Not meaning loss of drive air, more meaning loss of signal)
Example:
A flow controller and a fail closed valve. The positioner is direct acting. An increase in controller output opens the valve. Therefore you want a reverse acting flow controller to have negative feedback.
Now the same flow controller and fail closed valve. This time the positioner is reverse acting. Now no controller output means full positioner output and the valve is open. Full controller output means no positioner output and the valve is closed. Because the valve acts the opposite way (essentially, the controller thinks you have a Fail Open Valve) you now need a direct acting controller. Draw it out if reading it doesn't make perfect sense.