We stayed in Prague for 2 days at Ms. Sophies hostel (Recommended! At the Center of the City + Great service, Amazing rooms.)
We took the subway throughout this whole trip so I suggest you buy a one-day ticket. It could also be used from Tram as well. For sight seeing, I would suggest you take the tram. Although it is slower, you can see a lot more if you travel on ground.
We went sightseeing around the Prague Castle, the Prague Astronomical Clock and Charles Bridge. If you wanna take a nice photo, I suggest you wake up early and visit the Charles Bridge. People won't be too crowded in the morning.
I hope these tips will help someone. :)