Osaka - Kyoto - Tokyo in 8 days

Hi,
We arrive in April with 2 adults and 1 11-year old in Kansai for 8 days in Japan. Stay first in Osaka.
Go a day up and down from Osaka to Kyoto.
Travel from Osaka to Tokyo. Stay few days around Tokyo.
Leave on day 8 from Haneda airport.
- What is the suggestion: pick up JRpass at Kansai, use it for 7 days and buy last day separate tickets? Or? - What trains between Osaka, Kyoto and Tokyo are not covered by JRpass? (would be good to know when planning trip in HyperDia, or how can you see that in HyperDia if JRpass does not cover a certain train?)