Any suggestions on model and type of ski box to put on factory cross bars??

Are you talking the roof rails on an A3?

I just noticed that on the audiusa.com site, go to accessories, and they actually now have an option for factory roof rails. They even have a roof box.

I have the open sky model and the roof rack is the attachable type I got from the dealer

That thing sticks up so high, it should not be a problem for the Open Sky. Also, it sits outside the Open Sky System on either side. Just put it on and carefully open your sunroof while parked, for the first time.