I would go to the station Praha Holosovice and get on the train to Berlin that leaves at 9:00. About 14:00 I would decide if I wanted to get off at the Berlin-Schönfeld station or continue on to Berlin Ostbahnhof or to Berlin Zoological Garten, or even Berlin Spandau. Depends of course upon where you want to go in Berlin.
There are later trains at 13:00 and again at 15:00 that have the same schedule.

You will need to pay the difference for the mileage in the Czech Republic as, indeed, your Eurail will not cover that portion.

English language services are available in the Berlin Zoo train station. They should be able to assist you.

In Berlin Zoo or Berlin Ost station you can buy an add-on ticket from the frontier to Prague, or the same two ways. On the groun floor on the northern side of Zoo station the office of Euraide sells the same ticket and uses English. They have a website at http://www.euraide.de/.

Please write if I can help further.

Ben Haines, London

Oh nuts. I read the thing the wrong way. dyslexia strikes again. Mad Mad Mad.
Sorry about that.
There are 5 trains to Prague per day from Berlin that require no change of trains.
It will take a little money to buy the ticket from the German border to Prague.