Can you run "Full Analysis" in Fritz with a different engine? I have added Stockfish to the Deep Fritz GUI, and I even marked all engines except for Stockfish as inactive. However, when I run the "Full Analysis" it's still using Fritz.

Is there a way to use a different engine?
Go to Engine->Change main Engine... All you have to do then is select StockFish and click OK. Then click on New Game icon and the change will be applied, you should see title change from Fritz to StockFish. All that is left is to setup a position and run analysis...