I have edited a new book on Spring, Hibernate and Data Modeling which will answer your query on the design aspect of a Java EE web application. Typically a Java EE Web application has 5 tiers - client, presentation, business service, data access and resource(entity). The book focuses on how to design and develop each of these tiers by taking examples of all relationships of data modeling using Spring and Hibernate. As a download an entire web application is given where you would find information on managing each relationship of data modeling scenario.
Let's look at a simple standalone entity. In order to manage the entity, methods like create, read, update, delete and find all records have to be designed. So if we go bottom up, the entity creation forms the first step. Next we look at the Repository which has methods described above. Further up comes the business service tier and then the REST Spring controller which is JSON-based. The remaining task involves coding the JSP page and JQuery AJAX calls to the REST Controller.
You can find more information on the book here
