I just checked the Marix webpage (in Japanese)
http://www.marix-line.co.jp/index.htmIt looks like the lowest fare from Kagoshima to Motobu is 26,600 yen leaving Kagoshima at 6:00 PM arriving Motobu at 4:30 PM the next day. That's a one-way price.
On the other hand, you could use the Yokoso
http://www.japan-guide.com/e/e2364.html
and get a round trip airfare to Naha for the price of a one-way ferry ride. If you time your arrival right, you can catch a ferry to Motobu for about 2500 yen from Naha port.