Not real sure from your pictures what your question is about the window channel, but I believe it runs only on the sides (2 pieces per door) and not across the top. As I recall if you run the channel as one piece across the top of the window it would cover part of the garnish molding. The top of the glass with the window all the way up is tucked up high enough in the door that you don't get wind noise while driving.
Kent
