Travel with resident

Hello,
5 of us will be visiting, along with my daughter, who lives in Japan and cannot get the JR Pass. All 6 of us will be doing the following:
Day 1 Tokyo sightseeing
Day 2 Disney
Day 3 Disney
Day 4 Travel to Sapporo, Hokkaido (Lake Shikotsu)
Day 5 Lake Shikotsu
Day 6 Travel to Otaru, Hokkaido
Day 7 Otaru
Day 8 Travel to Narita for evening flight home

We don't know if we will fly or take the Shinkansen to Hokkaido. There is a 6 day regional pass that includes Tokyo and South Hokkaido (JR East-South Hokkaido Rail Pass) but not sure if it's the best option. Does it matter if 5 of us have the JR Pass and 1 does not? If we fly, is it better to do individual train tickets rather than a JR Pass?