The train service has been privatized and is operated by Arriva (a British company now actually owned by the German Railways). The service is called "Alex" [Oddly and unfortunately the site is only in German, its a job for google translator if you can't read German.] The "Prag Verkehre" section is the information for Prague and on this flyer(also in German).

I don't see specific pricing information, they encourage buying tickets onboard for cash (euros) or you can apperantly buy them in stations and agencies with about a €2 surcharge.

They do directly state the price of the return ticket special (2nd class, buy from the conductor on board). It costs €63 and children under 15 are free with an adult. So, if you just get yourselves on the train with €63 cash, that is the most you could have to pay (it is very possible that this return ticket is cheaper than one-way tickets for the both of you), and just throw out (or give away...) the return portion of the ticket.