I am getting close to putting my windshield and back window in as well. When I did my Challenger I was told to use a window channel primer (its black, comes in a can and has a brush); perhaps called urethane primer, I have some out in the shop waiting for me to use it. I believe it provides a better bound to the metal. The butyl tape goes on top of the primer, then the window on that. As for tips, I'd recommend putting the window in dry first and centering it up. Are you going to use the factory bottom wedges? if not then you need something to hold the window up (as in between the bottom and the top of the channel. When you test fit it you can determine the distance side to side, then you can perhaps make some small temp spacers to tape on the sides; with the bottom spacers and the side spacers you will get the window exactly where you want it. One other thing, you might want to find something that you can lay on the window to apply a little pressure overnight so that it sits right and sticks; that said when I did my challenger the glass guy that helped me merely pushed around the edges with his hand a few times and called it good but told me that he usually recommends putting something on them to apply even pressure so they seal. I've only had the Challenger in the rain once or twice and never noticed any leaks so I guess it worked.
Oh one other thing, I believe the butyl tape should start and end on the bottom in the center
