In my humble opinion, there are two basic ways Germany could have handled Austria-Hungary in TTL.
1) Germany could let Austria-Hungary crumble in a civil war and absorb both Austria and Bohemia into the Reich. Germany could then build an economic/military alliance with Hungary. Assuming that the regime in Hungary is able to remain in power (and considering the various minorities in Hungary that is no guarantee), then Germany should be able to form some sort of economic union/military alliance with Hungary and Bulgaria. A downside of this plan for Germany whether or not Hungary would be as loyal a client state as the Hapsburgs were in OTL.
2) Germany could maintain the Hapsburgs’ regime in Austria-Hungary. While it is true Germany might have to defeat the Hungarians in the event of a civil war, the prospect of having a single loyal client state would be worth the military investment. Keep in mind that in TTL, Germany is already going to have to deal with a lot of new regimes (Poland, Ukraine, Finland, and Lithuania) in the remnants of the Russian Empire. In terms of meeting German foreign policy goals, the Hapsburgs would most likely be the reliable regime in Europe.
1) Germany could let Austria-Hungary crumble in a civil war and absorb both Austria and Bohemia into the Reich. Germany could then build an economic/military alliance with Hungary. Assuming that the regime in Hungary is able to remain in power (and considering the various minorities in Hungary that is no guarantee), then Germany should be able to form some sort of economic union/military alliance with Hungary and Bulgaria. A downside of this plan for Germany whether or not Hungary would be as loyal a client state as the Hapsburgs were in OTL.
2) Germany could maintain the Hapsburgs’ regime in Austria-Hungary. While it is true Germany might have to defeat the Hungarians in the event of a civil war, the prospect of having a single loyal client state would be worth the military investment. Keep in mind that in TTL, Germany is already going to have to deal with a lot of new regimes (Poland, Ukraine, Finland, and Lithuania) in the remnants of the Russian Empire. In terms of meeting German foreign policy goals, the Hapsburgs would most likely be the reliable regime in Europe.