I have posted the sample itinerary that includes Kyoto, Osaka and Hokkaido before. But at that time, Hokkaido Shinkansen was not open. Current train schedule and operation are completely different from that time. At this time, I revise all train schedule and update the information. And I add many more detailed information and help you to build your plan much more.
Super Hokuto runs between Hakodate and Sapporo. This train is connected to Hokkaido Shinkansen at Shin-Hakodate-Hokuto. So if you move from Tokyo to Sapporo, take Tohoku-Hokkaido Shinkansen and take this train for Shin-Hakodate-Hokuto to Sapporo. Japan Rail Pass covers all these trains from Tokyo to Sapporo.