I haven't had any problems yet I wish I would have thought about that when I installed it and I would have put the empeg on the bottom.

Doesn't make a huge difference in the Golf - the lack of airflow is really the cause of the problem. To me the bigger benefit has been getting the empeg far enough below the cupholders so that I can still see the screen when there's a drink there. It's still worth doing when you get the chance IMO, but it isn't a magic bullet.