What is the Workbench?
The EclipseLink Mapping Workbench is a user interface for configuring the old EclipseLink native API meta data. It should not be used for JPA applications and does not have any support for JPA, JPA annotations or JPA orm.xml.
JPA applications should instead use Java or XML editors to define JPA annotations, orm.xml, and persitence.xml. Most Java IDE's have integrated JPA support.
The Eclipse Dali project provides JPA support included extended support for EclipseLink.