The first thing to do when designing the datastore layer is to define which of your classes are to be persisted (aka your "model"). You define this with either XML MetaData or annotations (or a mix of both). As well as defining which classes and which fields of these classes are persisted you also have to specify how the "identity" of each object is defined. When deciding which classes are to be persisted you also need to define if any classes interact directly with the fields of these classes. If so then these classes need marking as PersistenceAware.