Due to the age of my car and its original top, I also chop the canvas in the top above the window (which used to fold automatically, but now doesn't work so well). This keeps the canvas from coming into contact with the switch in the center and making a hole (which I already have and don't want it to get worse).
I also have problems with my top in that the top does not go into the black plastic track of the window frame, but goes on the outside of the frame... it's not only ugly, it stretches the top in odd ways and makes it far less wind and water proof.
Dropping my top requires at least three hoops for me to jump through, and I desperately want a glass window replacement top! They're just expensive and I want rims more than a new top right now
