Coincidence for me that this should come up. I just bought new weatherstrip for the sunroof on my 88 GT, planning on replacing it when I paint the roof (clear coat is pretty chalky).
My factory manual says something on the matter, but not much. There's a not real informative Figure 14, but maybe with the text it's enough to answer the question --
VENT GLASS WEATHERSTRIP
Install or Connect
1. Adhesive to gutter (40)
2. Adhesive to weatherstrip (35)
3. Allow adhesive to become tacky before installing weatherstrip.
4 Apply a bead of adhesive between outboard periphery of weatherstrip
and body opening (41) to prevent water seepage. Do not plug drain holes.
5 Watertest with a soft spray of warm or hot water.