Krakow to Prague

You can buy your tickets at the train station while you're in Kraków, and don't worry about your sefety. Looking at fellow travellers as potential robbers might make you look like a weird person.
There must be at least three of you travelling together, so when one or two need to use the toilet or go to buy beers, there will be another one staying in the compartment with the luggage.

Last time I was in the station there was an international counter which was very easy to find. I'm not quite sure if the older lady behind the counter spoke English, but it's worth a try.

You can indeed also book your tickets with ORBIS which has a branch on the market square, for an additional fee.

I would buy the tickets on arrival just to make sure that you get what you want although I doubt that the train will be booked out.

I'm with #1 when it comes to security issues. Your fellow travelers are the least likely persons to steal from you, it's rather people who just get on the train with local seat tickets roaming the carriages, usually these people don't fork out the fares for reserving a sleeping berth. You might also miss opportunities to meet locals.

As far as I know, buying two additional berths in a 6-berth cabin is not a guarantee to have the cabin for yourself. I think the conductor might have the right to put other people in when necessary; but I'm not quite sure about that. I recall taking a Polish night train in the 80ies where a woman bought a berth for her enormeous amount of baggage just to have that berth "confiscated" by the conductor for someone else, so that might have changed.

It's easy to buy, like the others said. The international tickets are sold in a building separate from the train platforms, but it is easy to find. I've been there a few times and the women speak English, so getting a ticket won't be an issue. Safety is good too, as stated above. Poland is a great place, and I've never felt better about travel anywhere.

Enjoy your trip, I know you will.

It's low-low season so there should be no problem getting tickets. First time on a night train? See www.seat61.com for photos and tips. Do get a couchette or sleeper (as these have doors that lock) and don't go cheap and use the seating section. In nighttrains I always take my wallet/passport and sleep on top of them.
... just two days in Krakow? Skip something else and spend more time there. Zakopane nearby is lovely that time of year.

You can buy tickets in advance from Deutsche Bahn, www.bahn.de. You can pay for them over the phone by credit card and the tix come in the post. Works out more expensive. Most likely you can just turn up in Krakow and buy tickets, and extremely unlikely to be fully booked but you could get allocated on different carriages - in which case you can talk to the conductor who will usuall persuade someone else to swap. If you're really risk averse and its vital for you to be together, then pay the extra and book ahead.

I think tix go on sale first 3 months before departure so you can't book Feburary yet - wait a month.

PS I have taken this train several times, mostly travelling alone (40 yo male) in 2nd class. The other people in my cabin were pleasant enough, friendly, never felt unsafe or threatened in any way.

Thank you all for your replies!
I really appreciate your kindness.
Really looking forward to my travel there!

Instead of booking through Orbis I would suggest booking through Bocho Travel on Stolarska street, just opposite the U.S. consulate, a few steps from the Main Market square. They don't charge any fee on top of the ticket price, are much friendlier and quite efficient in looking for special offers if there are any.