<persistence-unit name="pu1" transaction-type="RESOURCE_LOCAL">
          <property name="hibernate.connection.url" value="jdbc:database://url1"/>
          <property name="hibernate.connection.username" value="username"/>
          <property name="hibernate.connection.password" value="pass"/>
...
</persistence-unit>

<persistence-unit name="pu2" transaction-type="RESOURCE_LOCAL">
          <property name="hibernate.connection.url" value="jdbc:database://url12"/>
          <property name="hibernate.connection.username" value="username"/>
          <property name="hibernate.connection.password" value="pass"/>
...
</persistence-unit>

private static EntityManagerFactory emf1;
private static EntityManagerFactory emf2;

emf1 = Persistence.createEntityManagerFactory("pu1");
emf2 = Persistence.createEntityManagerFactory("pu2");


emf1.createEntityManager();//Will store to database defined in pu1
emf2.createEntityManager();//Will store to database defined in pu2