I've done a test with ground station with ipad with a naza quadcopter.
I've unplugged de propellers of the quadcopter.
I've connected the battery of the quadcopter,I've put on the dx8 sender.
I've created one waypoint on the ipad ground station.
I've selected "select all"
I've touched "OK"
I've touched "GO"
Result: the motors started
To stop the motors: I've disconnected the battery on the quadcopter.
Is there now still a waypoint in the memory of the quadcopter?
Do I have a problem to normal use the quadcopter next time or to configure next time
waypoints with the ipad?

Once you turn off the the quadcopter, the mission is gone, and it does not remember the mission unless you save the mission before you start
So if you want to fly with ipad the next time, please configure it again

Beside, if you test the ground station indoor, you may try simulation flight