The trim should have come off before the window came out.
You will need the plastic trim clips, butyl tape, a couple spacers used to keep it from setting too low.
First, clean all the old butyl out of the mounting flange. I used a Dremel with a small abrasive buff. Careful not to touch the body where the paint will show. I took it down to bare metal. Once you have done this, you will see little holes the plastic trim mounts go in. If there is still a plastic pin in the hole, just drive it in so it doesn't interfere with the new one. Next, I masked and sprayed the bare metal flange with a primer sealer followed by body color. Now, place the trim plastic and set the pins. Next, place the butyl tape around the flange. Finally, put the spacers in place to keep the window from being set too low. The inside edge of the window now gets coated with a black treatment to help it adhere to the butyl tape. Once that is done, you're ready to place the window. I did this by myself but you may want help to be sure it is evenly spaced side to side. Press around the edges to set. Finally, replace your trim.
As an optional step, you could have your trim straightened, polished and reanodized.
Then, just drive
and enjoy!