I don't quite get your question. Soft top back windows slip into the tailgate bar the slip into the two tailgate bar holders on either side of the tub then are secured by the tailgate. You can't put the tail gate bar in position with the tail gate being closed. Also with the tire in the way it makes it even more difficult.
'03 TJ Sport
/ D30/Ford9 / 35x12.5x15 KM2 / D window black steel 15x8 wheels / 3" custom long arm lift / SYE & 1350 DS / JKS BL / 1" MML / Smittybilt's front bumper, Tube fenders, Rocker guards, and rear bumper / High Rock Tire Carrier