well , thanks to your help we've been able to make EclipseLink JPA work with Atomikos and Spring, making it full JTA aware.
right now I cannot post the full source code, because we've been using it to test and try lots of things, and it would be quite embarrasing 
These are the steps :
1. Add these two properties to the EclipseLink factory Bean:
Code:
<property name="jpaProperties">
<props>
...
...
<prop key="eclipselink.target-server">my.spring.jtatest.AtomikosTransactionSessionCustomizer</prop>
<prop key="jdbc.exclusive-connection.mode">Transactional</prop>
...
...
</props>
</property>
target-server is the name of the class that will return an Atomikos UserTransaction when EclipseLink calls its method "acquireTransactionManager".
2. TransactionSessionCustomizer class
Code:
package my.spring.jtatest;
public class AtomikosTransactionSessionCustomizer extends JTATransactionController {
@Override
protected TransactionManager acquireTransactionManager() throws Exception {
Class<?> clazz = Class.forName("com.atomikos.icatch.jta.UserTransactionManager");
return (TransactionManager) clazz.newInstance();
}
}
3. Modify persistence.xml transaction-type to "JTA"
Code:
<persistence xmlns="http://java.sun.com/xml/ns/persistence" version="1.0">
<persistence-unit name="SpringJpaTest" transaction-type="JTA">
<jta-data-source>jdbc/MyDB2DB</jta-data-source>
</persistence-unit>
</persistence>
We had to add a dummy jta-data-source. Eclipselink complains if transaction-type is set to "JTA" and no jta-data-source is defined.
It seems that the name doesn't matter. Our datasource is not named jdbc/MyDB2DB and it still works.
Now we're trying to configure it with Bitronix. If we're sucessful i will post the results.
again, thanks simon1905 and GuyPardon.
without your help we couldn't have done it.