Vienna-Bratislava-Budapest-Krakow-Prague with children

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We will be travelling with children age 7, 11, and 13 (5 people total) in June with train travel likely in the cities mentioned above (in that order, although it could be changed if necessary). I have questions about prices, but also which web links to go to to order online.

Also, I believe the Budapest-Krakow and Krakow-Prague portions have night train options, and how much additional cost would it be to have a 6-person couchette.

Thank you.

First of all about straight forward fares (if you buy at the station before departure):
Vienna-Bratislava (14 euro - EURegio ticket, regional trains from Wien Sued.), Bratislava-Budapest (one way 12 euro, return - 16 euro), Budapest-Krakow (app. 60 euro ticket + 9.4 euro 6 berth couchette), Krakow-Prague (37 euro ticket + roughly same 10 euro for 6 berth couchette)
As you can see there is only one pretty much "expensive" part of the journey - BP-Krakow, but you can avoid paying such price with two possible options:
1) In case you will stay more than 3 days in BP you can try to purchase special discounted Spar ticket Budapest-Krakow (39 euro, couchette supplement already included)
2) Do a really simple trick - while in Bratislava purchase return ticket Bratislava-Budapest for 16 euro + Bratislava-Krakow ticket for 45 euro (you will use it on your way from BP to Krakow). And all you need to do additionally in Budapest is to purchase couchette supplement BP-Krakow.
Unfortunately for you there is no chances to purchase tickets for your journey online directly from train companies - neither Hungarian, Slovak, Polish railways sell it in such way. The only tickets which you actually buy online is for journeys originating from OEBB or CD - Vienna-Prague, Vienna-BP, Prague-Krakow, Prague-Bratislava/Budapest etc.
But actually the fact you can't purchase it online isn't that big of a problem - trains in Eastern Europe isn't that full, so I would not worry at all, especially due to the fact, that you will need seat/sleeper reservations only for two legs of you journey (BP-Krakow and Krakow-Prague)