Marty's technique should work fine.
You can also use the twine/string technique described in the Shop Manual (Body section) for installation of a windshield. That technique also works fine with the panel door windows.
I used the same method as used with windshields.
The installation is easier if you have a helper.
If you use a lubricant, it is a good idea to use a rubber lubricant (like the type sold for use with brake cylinder rebuilds), or a water soluble lubricant (like K-Y Jelly).
By the way, many people suggest having this done buy a professional glass installation shop. My experience is that most installers younger than 50 only know how to install modern glass, using silicone sealer (and simply placing the glass in place against the sealer). Often these installers will not admit to their ignorance and they will really mess up an old style seal and installation.
Is your seal a one piece seal with no joint or a one piece seal that you have to cut to fit? If it has no joint, where did you get it? If it has to be trimmed to length, cut it at least 1/8" longer than what you need - it will shrink.
Tim