1st visit to Japan

We are a group of four (2 adults and 2 small children) and will be arriving Narita airport late 8:00pm of 3/22/10. After pick up the luggage, and activate the JR passes, perhaps 9:00pm before leaving NRT to Tokyo. We will be heading to Intercontinental Tokyo Bay hotel.

1. Which transportation will be best in your opinion, (airport bus or Express train) and still available at this late ? I am rather concerned because of two small children and also luggage to pull along. Is there an airport bus that will take us directly to this hotel door ?

2. Could you give suggestions - what places to visit for the two days in Tokyo (that would also satisfy the two kids age 6 and 10 ? They are crazy about Manga and Hello Kitty.

2. After 2 nights, we will be heading to Osaka (and stay there for 3 days), using the JR pass. Do we have to make reservation for the JR bullet train ? When should I do that and who to contact for reservation ? We prefer to leave in the morning, what time should we leave ?

Thank you.

1) Direct Limobuses are available during daytime. But not that late a night.
http://www.limousinebus.co.jp/en/platform_searches/index/2/48

So, you must take a train to JR Tokyo. The Airport Express (or NEX) departs from Narita Airport Train Station at 20:44 or 21:44 and arrives at JR Tokyo station within 1 hour. As you doesn't seem to travel on budget, it's advisable to take a taxi from there to your hotel.
http://www.intercontinental.com/intercontinental/en/gb/locations/maps-...

2)
http://www.kiddyland.co.jp/en/index.html
http://www.puroland.co.jp/english/welcome.html

3)
As the seat reservation is free with JR Pass, you don't have to use unreserved seat. Just go to the JR ticket counter(Green Counter) at JR Tokyo or Shinagawa Station and book it on the spot. The Hikari Shinkansen are operated twice per hour.
http://www.japan-guide.com/e/e2018.html