As in every other European pub or restaurant, it is customary to tip good or acceptable service in Prague. In pubs, the Czechs themselves tend to round off the bill to the nearest 10 or 20 kc. So if a bill is 78kc you might tell the server to take 90kc. It is also possible to leave a tip on the table but in general if you are paying the server directly then you give them the tip as you pay by telling them how much to take in total. If they leave the bill on the table (which is more common in restaurants) and walk away then it is quite normal to leave the price of the bill along with the tip on the table.
The size of the tip is generally left up to you. So in a pub the tip might be quite small but in a more expensive restaurant the tip should probably be a bit larger. It isn´t necessary to get out the calculator to work out percentages if you feel the tip you are giving reflects your satisfaction with the service.