Amsterdam is a bit far away from Prague by train (although I haven´t checked the different cheap air companies in Europe, there might be a possibility ...). As you want to fly into one city and leave from the other, I think that you have two options : Vienna and Berlin.

An EC train runs from Prague to Vienna around 6 times per day, leaving from Praha Holesovice and arriving into Wien S�dbahnhof. It takes around 4 and a half hours. From Prague to Berlin there is also an EC train that takes around 5 hours. It leaves from Praha Holesovice to Berlin Ostbahnhof.

You shouldn´t have any problem buying your train tickets in Prague. Go to the Cedok office in Na Prikope. They speak english, accept credit cards and they also have good prices. http://www.cedok.cz/incoming/index.asp

And if you want to check train schedules, I have always found the german railway site very helpful : http://www.bahn.de

Good luck,

Covadonga Bilbao - Spain