Hi there Louise,
Unfortunately there is no combined railway ticket that covers all of your stay. Firstly, Hakone is not a station covered by the JR Pass and is not situated near any shinkansen lines. My recommendation would be purchasing a 2-day Hakone FreePass, with the round trip included. This leaves from Shinjuku station and returns there, and can be purchased online or at any station with an Odakyu terminal (such as Shinjuku). Also, child fares for this fare are heavily discounted.
Since most Tokyo metro lines are privately operated, if you're relying on it for travelling around the city it's worth looking into getting a prepaid travel card, such as a Suica card. Your Japan Rail Pass already covers you for travel on the circular Tokyo Subway JR Yamanote Line, but if you want to access the 13 Metro lines that run off of it a card will come in handy. The choice is yours regarding which one to get; more info on this can be found below:
https://www.jrpass.com/blog/benefits-of-prepaid-travelcards
As for travelling between Tokyo and Narita, it's easiest to just buy the tickets regularly.
Hope this helps!
Alexis