You don't say what web site you're using so it's difficult to give advice.

raileurope is one I've looked at. I know its too early to book, but I am not sure how to do it.

Raileurope does not give all option and they charge more than booking directly with the country rail web sites. Here's the site for Hungary:

http://www.mav.hu/english/index.php

You can wait until you get to Krakow to book your train to Prague. There's only one night train that does not make connections. It leaves at 21:54 and arrives at 7:50.

You can look at all schedules on the German train site:

http://www.bahn.de/i/view/USA/en/index.shtml

Polrail has been recommended on this board for ticket booking:

http://www.polrail.com/sections/store/quoteprice.html

I just remembered that there was a recent thread about booking through Mav for Hungarian tickets. The person said that after he booked and paid for the ticket (Romania to Budapest) he learned that he was expected to pick it up in Budapest at a kiosk. So watch out for something like that before you book. He could not get a refund on his ticket. I don't know if he did something incorrect in the booking or if the site does not sell etickets.

I just took the train from Krakow to Budapest on May 20-21 and it worked out great, except for all the banging to separate and reconnect the train along the way.

I booked on Polrail and paid with a CC. Polrail had emailed me when the tickets became available and I booked a two person sleeping compartment. I had the tickets UPS'd to my house and had them in 3 days. I then got an email that they were able to book the discount SparNight rate, so they credited me a rebate.