* The "haven" itself: The entire concept of Fablehaven as a secret sanctuary for magical creatures can be seen as a metaphor for the hidden wonders of the natural world. It suggests that there are amazing and extraordinary things existing beyond what we can see on the surface, waiting to be discovered.
* The "Fablehaven family": The way Kendra and Seth's family struggles to keep Fablehaven a secret, and the way they each have their own role in protecting it, is a metaphor for family responsibility and the importance of working together.
* The "animals" as representations of human nature: Many of the creatures in Fablehaven, like the mischievous sprites or the powerful, yet unpredictable, dragons, can be seen as metaphors for different aspects of human behavior and personality.
To find a specific metaphor, you could think about what aspects of the story, the characters, or the setting are being compared to something else. Do you have a particular part of the book in mind?