There are sensors in the partition in the trunk.
Make sure it is seated right or you will get the beeping and it won't work.
Take the partition down...stick your head in the trunk now reassemble the partition you will see it if you look.

When you turn and push the top up its like its springs to the right position.

And when putting the top down hold the button down til it beeps at you that its done.

If you keep on the button after the top is down,both windows will go up...no biggy just let go of the button and push the individual buttons to put the windows down.

Make sure you get that beep after putting the top down....it makes sure the hatch is latched.

Also if you are going to fast the top won't go down and the car will beep at you then also.....there is a way to bypass this feature.