Kyoto has many hotels and tourists. You can book a hotel by yourself on a booking site.
The conference booked rooms in a reasonable hotel, Coop-Inn Kyoto, from 15 to 21 September. (Their Japanese website has more pictures.) The hotel is located in the city center of Kyoto. The room fare is as follows with no hidden extra charge. One breakfast costs 500 yen.
On the Conference Venue
The conference will take place in International Conference Hall III of Clock Tower Centennial Hall in the Main Campus of Kyoto University. The Clock Tower Centennial Hall is located just after the main gate of the university and thus is quite visible from the gate. The building is numbered 3 on this map. The conference room (International Conference Hall III) is on the second floor (first floor for Europeans) of the building.
To Kyoto City
Kyoto has two convenient airports, which are located in Osaka, a neighbour prefecture.
The other is Osaka International Airport (ITM), which is often called Itami Airport. In spite of the name, it serves mostly for domestic flights. You may fly to this airport via an airport of Tokyo – Narita (NRT) or Haneda (HND), both of which have many international flights. Actually ITM is closer to Kyoto than KIX is. To get from ITM to Kyoto, see this page.
Most buses from both airports for Kyoto end in Kyoto station, but some evening buses go into the city center.
If you stay in Tokyo before or after the conference, Shinkansen (high-speed railway line) is more convenient than air planes.
To Kyoto University
The Main Campus of Kyoto University has two convenient bus stops: Kyodai-seimon-mae (which means Kyoto University Main Gate) and Hyakuman-ben. The former is closer to the conference building. Kyoto has different bus companies, which would be confusing for visitors. Kyoto City Bus, run by the city, is major and convenient. (Please don't confuse it with others, in particular "Kyoto Bus"!) The information on Kyoto City Bus is found here.
Convenient bus lines for Kyodai-seimon-mae are #201 and #206 of Kyoto City Bus. Otherwise, #3, #17 and #203 go to Hyakuman-ben. You can choose one of those depending on your hotel (Coop-Inn Kyoto has a bus stop for #201). Those lines are relatively frequent. During the day time they are scheduled to come every 15 minutes at least. This route map of their buses would help you choose a line and a hotel. To get from Kyoto station to those bus stops, see this page.
If you don't mind walking a little, Demachiyanagi station on Keihan line is the nearest train station to Kyoto University. The line does not go to Kyoto station, but your hotel may be located along the line.
If you love walking, the path from Imadegawa station on the subway Karasuma line to the university would be pleasant. You will see the Kyoto Imperial Palace and cross a bridge on Kamo River on the way. It takes about 30 minutes.