Our family is going to Japan this summer. I have been reading about transportation options, but I am having a hard time comprehending what would be the best way of getting around.

We are flying into Osaka and staying at the Renaissance Naruto Resort the first night. Their directions are to take the express bus to Tokushima, get off at Kosoku-Naruto bus stop, then take a hotel shuttle bus. Since we get in late in the afternoon, we we stay there one night before going on to Kyoto.
I think I read that we should take the train to Kyoto. We will stay there 3 days at the Watazen Ryoken. I read that the best way to get around Kyoto is by bus, and that you can buy all day passes. I know there is lots to do there. Are their any arrangements I should make ahead of time?
Next we will go to Tokyo, and stay at the Courtyard Ginza. We we fly out of the Narita Airport on the way back to the states.
Do I need to buy or make train reservation before we arrive?
Any advice would be appreciated.
Darlene