It makes sense to start your trip in altitude in the sacred valley, either in Ollantaytambo or Aguas Calientes. There is a hotel in Olla just beside the train station, not really cheap, but good value for money (at least 2 years ago), but should find in both places rooms at a wide range of prices.

As for tickets to the Huayna Picchu, it might be best to get them the day before, they usually reach the limit before 7am.

To visit sacred valley/Cuzco, 2 days is rather short, there are many many sights to see, try to be on a Sunday in Pisac to visit the market (as well as the archeological site, if you have time).