It must be initialized if you disengage the motors. There are 2, btw.
Get the top in the stowed position, have someone hold down the storage lid, and hold the switch in the closed position for about 10 seconds or so. It should pull the storage lid down. Done.
I think that's how it works........its been a while.
And the problem with the top getting stuck is probably due to the tensioning straps being too weak-common problem, expensive to fix. When it gets jammed, notice that the storage lid is hitting the rear bow of the top. Go back and pull the second from the last bow towards the front of the car, and then the rear bow will be able to move and clear the storage lid.
The straps are weak, so it needs help pulling the top forward out of the way of the storage lid.