Any updates on this? In 2013 we were in Vienna, Prague, Brataslava and Munich. U Fleku was cool as was U Vejvodu which is a very big bierhall. There was also a small brewery called Pivovar U Tri Ruzi (at the three roses?) which had great beer and of all things... great burgers too. I also found a beer in the Czech Republic called "Bernard" which I had never seen. It came in a Grolsch-style bottle and a waiter where I was drinking it said it came from the southern part of the country. I hope the OP's trip was fun!
Pivovar Bernard is partly owned by Duvel. (Same as Boulevard)
And is in Humpolec (central Bohemia). Since they are owned by Belgians they make some fruit ales but majority or production is good old Czech Pilsner.