At first, you should approach Nagano. You can use the Asama Shinkansen from Tokyo or Limited Expres Shinano from Nagoya, both trains are direct, so you need not change train. At Nagano just take the train to Yudanaka. This line is not JR, but it starts from the underground stage which is in few meters distance from the JR station building. And finaly Shibu Onsen is around 20 minutes of walk from Yudanaka station along the river upstream. Or 3minutes by car (hotel staff pick up us)

Stepan