The Graveyard Book is an interesting story that reflects on themes of family and fate. There are quite a few other interesting themes this novel addresses, but the most crucial theme of the story seems to be the role the community plays in raising a child. This ties in with the theme of fate versus free will.
Let me explain:
The story starts out with a horrible murder. Ronald Dorian (an architect), his wife (Carlotta), and their 7-year-old daughter (Misty) are fatally stabbed to death by the mysterious and evil Jack Frost. Jack belongs to an organization called The Jacks of All Trades. The reason Frost has been tasked with murdering the whole family is because someone in the fraternal order prophesied centuries ago that the day would come when a special child who could walk the borderlands between the living and the dead would destroy the whole order.
Alas for Frost! He bungles the job and doesn't kill the child after all. Nobody Owens (as he comes to be called by his new graveyard family), survives. He is nicknamed Bod for short. The dead inhabitants of the graveyard speak their mind on whether they will take Bod on as their own after his mother's ghost pleads for Mrs. Owen (who becomes Bod's adopted mother) to protect her son from Jack Frost. So, you can see that the graveyard community (or all the interested parties) come together to carve out a consensus. Mr. and Mrs. Owen become Bod's new parents. Silas becomes his special guardian. Miss Lupescu, a Hound of God, is another special guardian and teacher. Bod inherits teachers, playmates, aunts, uncles, confidants, brothers, and sisters from this community of the dead.
Bod learns special skills from many of them. Besides all the subjects you typically learn in school, Bod also learns how to Fade (to become visible and invisible as the situation requires), to DreamWalk (where he is able to enter the dreams of another person), and how to cry for help in different languages (this last one is taught to him by Miss Lupescu). Bod is given the Freedom of the Graveyard; this is the ability to come and go as he pleases to any area of the graveyard, be it tombs, private mausoleums, or secret crypts.
So, how does this tie in with the theme of free choice and fate?
It is Bod's community of care-givers and mentors who prepare him for the final battle to defeat the order of The Jacks of All Trades. They do everything possible to provide him the necessary tools to thrive and to succeed; Bod's part is to decide whether he will eventually face the evil he has been prophesied to defeat.
Hope this helps!