Seeing the historical city where the famous sights are located is a must. Going there early in the morning or late at night is much more pleasant, as you will avoid crowds of tourists. Once you have visited the major places (allow yourself at least one full day to do that), take it easy and explore some of the non tourist parts of the city. Žižkov is a bohemian part of Prague with a unique spirit (where pubs are found literally on every step). You can also spend half a day in some of the popular local parks that come alive in summer when the beer gardens open (e.g.Letná, Stromovka, Riegrovy Sady, Vyšehrad or Vítkov). Another option to take a break from walking around the city is renting a paddle boat. The view from the river is pretty amazing.