Most valve actuators have a method to disengage them so they can be turned manually. I know on the Goldline and Jandy actuators this is done by putting the switch on the actuator in the off position, unscrewing the locking know 4 turns and pushing down on the knob to disengage the gears. The valve can now be controlled manually but will not work automatically now.
To restart automatic operation pull up on the valve handle and turn it to the left and/or right until you feel the gears engage, tighten the locking knob, and put the switch back to whichever on position it was previously on (on1 or on2).
For other makes of actuators consult the instruction manual since they will have different ways to manually move them.
NEVER TRY AND MOVE A VALVE ACTUATOR WHEN IT IS ENGAGED AND IN AUTOMATIC MODE or you most likely will break it!
If you want to move the valve with the system running you can flip the switch to the other on position and then to off when the valve is where you want it but be sure to turn it back to the original on position when you want to resume automatic control or you might have some problems (like accidently drainging your pool and overflowing your spa at the same time!)