I stayed just two nights and found Church Pension pleasant and well-located. I arrived mid-evening and reception was no longer open but the guard on the main door had my details and the key -- I was impressed by the efficiency. My room was for 4 but I was the only one in it -- lots of space to spread out. Showers and toilet were just down the hall. They were always clean and I never had to wait. Breakfast was included -- typical European fare, plenty of it and served with a smile.
It's 15-20 minutes walk from the main train station and the same from Old Town Square. The No 22 tram is a short walk away and this takes you right up to Prague Castle -- a great scenic ride.
There are restaurants and small grocery stores nearby. For dinner a couple of bread rolls, smallgoods, cheese, fruit, and a beer from the local grocery was enough for me -- and really cheap.