Don't worry about the trains, thats the least of your problems. All the train stations I've been to so far are easy to figure out. Just follow the signs and pay attention!!
If you can't figure out how to get somewhere ask the Eurohelp(sp?) desk. They speak perfect english and can get you anywhere!
To get from Frankfurt to Prauge you'll most likely have to connect thru Munich, or atleast pass through it.
I've been a wild rover for many's the year,
And I've spent all me money on whiskey and beer.
But now I'm returning with gold in great store,
And I never will play the wild rover no more