I've found that elmer' pro-bond or gorrilla glue works better than silicone for adhereing the cork to the glass...the problem I always had with silicone is no matter how much I rinsed it off, when I tried to use silicone on it, the silicone just gathered so much dust it wouldn't stick to anything any more...the pro-bond doesn't have that problem, also the pro-bond and the great stuff are both made of poly-eurethane, so they are extremely compatable.
You can also flatten the cork (a little) ahead of time, I usually soak it in water, then I screw it to a piece of plywood, any where I wan't to flatten, I just sink a screw. After the cork dries again, I take it off of the plywood.
A lot of people also cut the cork up into smaller pieces, and then glue them on.
Hope this helps,
Brian