Just buy your ticket at the train station before you get on the train.  Buying a ticket at the border would be a nightmare.   Since most everybody working for the railroads in the Eurail countries speaks English, it’s slightly easier to buy the tickets in Germany (or whereever) than in Czech Rep.  Just show your railpass and tell them you want a ticket from the border to Prague and from Prague to whichever border city you’ll use.  You can find out the border crossing by clicking on your specific train on the German rail website: http://reiseauskunft…

Some sites that sell railpasses sell a “Prague excursion pass” that’s good from any Czech border to Prague to any Czech border.  It’s slightly more expensive than buying the tickets in Europe, but not too bad a deal if you buy it with your railpass so you don’t have to pay additional shipping.  You can also buy the ticket from the conductor on the train, but it will be more expensive (because it includes a small fine) and you’ll need to have Czech Krona (preferably exact change) with you.