installing quarter glass on coupe help

this is probably a simple thing to do, but i just dont understand what to do. i have a 86 coupe and i have 88 coupe style quarter glass i want to put in, but i noticed that like 3 of the bolt studs do not go through a hole or anything, what did you guys do to keep a good seal? thanks
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you need to mark and drill the holes, I would use some kind of silicone sealer around the holes but its probably not needed if you use all the fasteners