My hardtop was the opposite. The seal went on the glass first. Then a piece of rope went around the seal (where the hardtop goes). Put the window in from the inside and used the rope to pull the seal around the hardtop. I had a friend's brother who works at a glass shop help me out and he had some tricks to make it easier, but I can't remember what they were.
77 CJ-7- AMC 360, Edelbrock cam, MC2100, Fenderwells, CJ T18/D20, Chevy D44/EB 9" rear, Trutrac f/r, 4.11, SOA, 1.25 lift shackles, 35x12.50 BFG KM2s, Shackle Reversal