On my first Interrail I had nothing booked in advance and, although I didn't ever have to sleep in a railway station, it was unnecessarily stressful. I think it may well be pretty tough to find hostels in those popular places at this time of year without booking.
If you do book ahead you'll have less flexibility but less strain of walking around trying to find somewhere to sleep after a long train journey.
This year I booked all of my accommodation in a couple of evenings and it all went like clockwork. The only hassle was making sure I caught the right trains, which is just part of the Interrail experience anyway.
You can easily book in advance through hostel booking websites and, if you do want to extend your stay somewhere, you can email the next hostels and hopefully reschedule your stays or find alternatives.
I've just returned from a months travel and found that 2 or 3 nights were adequate for exploring a place and, if you don't like somewhere, you will be moving on soon anyway.
For Prague you can try the Welcome Hostel Hlavcova: it's, quiet, near the river, and is 20 minutes on foot from the old town. I had a single room there last month for 17 GBP a night.
Have a great trip.
:arrow: Hostel booking here: rail.shop/hostelworld