best use of rail passes

I will be flying in to Kansai Airport with my Family comprising 2 adults and 3 children.
We will spend 3 nights in Kyoto, 1 night Hakone, 4 nights Tokyo and then fly out through Narita.
It seems that the 7 day JR nationwide rail pass will not be cost effective.
I have worked out:
1.Use JR West Pass- Kansai to travel from Airport to Kyoto.
2.Use Hakone free pass (purchased inside free area)
Please could someone advise me on the best method to travel from Kyoto to Hakone, then from Hakone to Tokyo (shinjuku), around Tokyo and then to Narita.
(Also please confirm whether my assumptions above are on track)
Thanks very much

Yes, your assumptions about rail passes are right.

Please could someone advise me on the best method to travel from Kyoto to Hakone, then from Hakone to Tokyo (shinjuku), around Tokyo and then to Narita.

From Kyoto to Hakone:
http://www.japan-guide.com/e/e5206.html?aFROM=2158_5200

From Hakone to Tokyo:
http://www.japan-guide.com/e/e5206.html

From Tokyo to Narita Airport:
http://www.japan-guide.com/e/e2027.html

I would say that you have got the equation correct on the use of tickets. Kyoto to Hakone probably best done by train from Kyoto to Odawara. Take a shinkansen to Atami and change to a local Tokaido line train to Odawara. Y11550 adult . Local trains run every 20' and take 22'. Get your Hakone passes at Odawara. You can come back to Odawara to catch a shinkansen to Tokyo or finish your Hakone sightseeing at Mishima and take the shinkansen from there. From Odawara Y3440 from Mishima Y4200 . You could save a few dollars buy taking local trains to Tokyo but it wouldn't be worth the time and aggravation.