Hi Phil, I have put in windows on several of my cars.  The best thing to do
is wait until a hot day to do it so that the rubber is soft and easy to work
with.  Some people use a silicone lubricant but I have never tried this.  
1. Fit the glass into the new rubber seal. 2. insert a small rope into the
groove in the seal where it will eventually go into the sheet metal (make
sure this rope has excess of at least 7 inches on each side once in) 3. With
one person inside with the "rope" and the other outside holding the glass in
place, pull the string starting at one end and have the outside person follow
the string with firm pressure to seat the window. 4. Once the lip of the seal
has been extended over the sheet metal go outside and using the heel of your
hand pound the glass around the perimeter to make sure it is fully seated.

That should be it, good luck!

-Loretta
87 Syncro
90 GL