You should be ok, and be able to get to Prague quite cheaply.
Your worst case scenerio would be to buy two one-way tickets from Frankfurt airport to Kahl (about 6 or 7 euros each). Kahl is the first stop in Bavaria.
At that point you will need a Bayern ticket (about 28-29 euros). This single ticket will cover the two of you all the way to the German/Czech Republic border.
At that point you can buy two tickets to Prague. Czech trains are inexpensive.
You can buy your Bayern tickets online at Die Bahn.