How to use hibernate with complex applications ?

Suppose I have several .ear ( or .jar ) files with some hibernate
classes/mappings in base .ears. New .ear files are new modules
of complex application and can be deployed on the top of base .ear . The example is a parented deployment in Oracle Application Server.

How to organize separate hibernate ORM , such as if one class has assosiation/subclassing to another classes in parent .ear ?

For now, it seems I have to have everything in just one application .