Ok i figured it out. I put the window half way and put the rubber section that ultimately will go in the door panel and slid it behind the glass itself and then pushed it down to the bottom. Then from in the door cavity I pulled it down and pushed it into the channel where the window stays in. Once i did that i just pushed everything into place and I was golden.
Next is to put in the passenger side. Hopefully tomorrow with a test of the window noise.