Why not a hostel mate?
We've stayed in one there and it was fine.
They have different sized rooms, some with a bathroom to yourself. Someone comes in to clean too. Let's face it, you won't be there much
http://www.hostelatlas.cz/
It's right across the street from the best strip club ever - darlings - and the road leads straight on to wenceslas square.
Oh, and prices start at less than a tenner a night per person.