Java EE (6) is an abstraction of existing products (Hibernate, TopLink, Glassfish, JBoss, Geronimo, Tomcat+, ...) and API-implementations. So if you develop Java EE 6 applications, you can start with the spec and dig into the implementation details as needed. If you are using e.g. Glassfish application server, EclipseLink (JPA), Equinox or Felix(OSGi), RedHat Weld (CDI) ... are working for you - but you don't have usually to care about the details.
The best of all - if you don't like a certain implementation - you can change your application server. After learning plain Java EE (5 or 6 - both are similar), you will be able to work with all application server vendors with minimal learning curve. This year I would expect at least 4 Java EE 6 server implementations: Glassfish 3 (is done), JBoss 6 (not yet), Geronimo (announced), Resin (only parts - but sounds interesting).