One box should have all the windows rolled around a big cardboard tube with paper separating them, the other should have the door surrounds, big plastic knobbed thumb bolts to attach the surrounds to the cage and the plastic things that clip over the tub and secure the bottom of the rear window.
That was for a 2 door, 4 door should be similar but they have extra surrounds and a few bolts I believe to attach the rear surrounds.
Picked up the new ride on Friday. Went through everything with the sales guy and all was well regarding the top. Got it home and hoisted up the hard top and removed the soft top and stored it away. First time doing that. It went fairly well. I used i-bolts in the ceiling and ratchet straps.