I don't know if my methods are the correct way, but my stuff has not leaked a drop.
1970 Charger. For the rear glass, I laid a 5/16" butyl rope on the window channel about 1/4" inboard of the edge of the metal flange, then set the glass on top of it. I had metalwork done in the channel so I knew that there would be some uneven spots that would not seal with that butyl stuff alone. After setting the rear glass in place, I squirted that gooey black sealant around the perimeter on the inside and spread it with my finger, making sure to fill all gaps. ZERO leaks and the interior trim pieces cover the sealant edges.
For the front, I put sealant on the entire perimeter of the window channel AND on the inner channel of the gasket where the glass fits into. I set the windshield gasket to the opening and hold it in place with duct tape then set the glass in, bottom first. I use a plastic spoon/paddle to work the glass into the channel working from the bottom up. It takes me awhile but after the glass fits in the channel completely, I use a new rope lock strip.
Again, there may be other methods that work other than mine. I may be overdoing it with the sealant; others might only use it in the bottom corners. I just figure the tube will harden in a few months if there is any sealant left in there, might as well use it up.