I have seen some tutorials that explain how to get joins to work between two tables, but I am not sure how to reference them correctly. Mostly because this tutorial does not tell what the fields are in the tables:
http://docs.jboss.org/hibernate/stable/ ... ryhql.html
But rather assumes you know the structure. Anyway, if I have a Material.java file which has @table(name=material) and a MenuMapping.java file, with @table(name = menumapping), how do I create a join of the two tables inside of the Material.java file. How does the material.java file know there is a table called menumapping? Or do I just reference the MenuMapping class (do I need to import it)? How do I set up the files to make these types of hql calls?

Well, you need to know if you have a one to one, one to many, or many to many relationship between the entities. You should have foreign keys in your db, and you'll have instance variables for reference in your Java classes.

Here's a good tutorial on doing a one to many mapping with Hibernate:

http://jpa.ezhibernate.com/Javacode/learn.jsp?tutorial=18mappingonetomanyassociations

That includes the ERD and the class diagrams, so you'll get a good idea for what is going on.