The mid gate consists of 3 parts... The Lower part that has the hinge etc, the middle part is the bar that the window goes on top of, and the window.
When the window is removed there is a switch/lever that pops out that then allows the bar to move with the lower part of the midgate.
If the window is still sitting in place the switch/lever is pressed in which prevents the bar from moving with the rest of the midgate and stays in place to hold the window.
So yes enoniam is correct. You do it the same way with window in or out, just that the bar will stay or move with the rest of the midgate depending on if the window is in or not. If the switch/latch is broken or sticking it may not allow the bar to stay in place thus your window has to be removed to drop the midgate but otherwise should work fine.
Rodney