I have started the process of updating, syncing, etc. You need to set aside a good bit of time to do this. Remember what it was like to sync an iPod or iPhone the first time?
You will need to play with some of the settings to get them right. Take your time. It is very tempting to hurry things up.
While everything is syncing, consider which apps you want on which screens of your iPad. I am trying to have only about 3 horizontal rows of apps on each page.
As to iBooks, you will find a pleasant surprise in your library. Winnie the Pooh. It even has the watercolor pictures.