Just walked my brother in law who lives in NY through this. The first time you take the hard top off and try to put the soft top up, it will be difficult to latch to the windshield.
There will be two plastic pieces which are square and this is what the bar of the rear window will go into. He called me because he claimed there was a gap between the bottom of the rear window and the tailgate and things weren't lining up. There will be an indented area on each side of your tailgate that is where these should insert. Your sails will still be able to be attached on the bottom. Hopefully this helps. Not sure what else you have in the box.