How to travel to Hakodate and Sapporo

I am planning my first visit to Hokkaido from Tokyo next year. My plan is to visit Hakodate and Sapporo, both for 3 days.
According to Google Maps, I can take the JR Tohoku/Hokkaido Shinkansen from Tokyo Station and travel to Shin-Hakodate-Hokuto Station and then take a local train (Hakodate line) to get to Hakodate. I understand the JR Pass will cover the cost of the Shinkansen ride, does it also cover the local train ride from Shin-Hakodate-Hokuto Station to Hakodate Station as well?
Also, for my second destination city (Sapporo), is there a Hokuto Limited Express in Hakodate Station that can take me to Sapporo? If so, does the JR Pass covers its cost?
After I stay 3 days in Sapporo, I would then travel back to Tokyo from Sapporo. Can you suggest to me how I can do it by rail? I ask because Google Maps show me a very long return route compared to my entry route.
Overall, do you recommend that the 7 days JR Pass is worth it for my return trip from Tokyo to Sapporo?