September is an excellent time to visit the Painted Hills, since the days will still be sunny but cooler and more comfortable for seeing the sites. The main site of the Painted Hills, one of 3 units in the John Day Fossil Beds National Monument is just outside of Mitchell, OR. This is where you’ll find the closest lodging as well as restaurants.
This website gives you a great overview of the area with photos. http://mitchelloregon.us/
Here are links to available lodging:
The Oregon Hotel http://www.theoregonhotel.net/
Painted Hills Vacation Rentals http://www.paintedhillsvacation.com/accommodations.htm
Sky Hook Motel http://www.visiteasternoregon.com/entry/skyhook-motel/
The Painted Hills Cottage http://www.homeaway.com/vacation-rental/p164794