If you are in a traditional Czech pub – pivnice – and you want another, just finish your beer and sit where you are and you will be brought a fresh one, without asking.
If you want to go, call for your bill and pay before finishing. This is normal practice in Prague. It’s not a trick on tourists. If you don’t go with tradition and end up with a beer you didn’t want, you can try giving it back to the waiter, but I think you might lose this one.
One thing that often stumps Americans visiting is the whole tipping thing. Generally, Czechs don't tip. They simply round up from their bill, so 37kc becomes 40kc. it used to be that if you tipped 'well', like 10% or more, the next time you came to that place they treated you like crap. Within their cultural context, you were showing off and a prat and deserved a hard time.
Nowadays this is changing somewhat, especially in Prague. People have become accustomed to making a little extra cash by at least feigning interest and politeness. But I still wouldn't tip more than 10%.