Markus,
You would do this with two different AdWords accounts. You would also have to have the domain for both Austria and Germany registered and live even if its the same exact site.
Germany > AdWords + Merchant Center (Analytics for the .ge)
Austria > AdWords + Merchant Center (Analytics for the .at)
You would end up creating two different product feeds and the country of sale and target countries would be different. Let me know if you need any more advice on this.