No persistence.xml, você pode se refirir aos schemas:
<persistence
xmlns="http://java.sun.com/xml/ns/persistence"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
version="2.0" >
<persistence-unit name="schemaOne">
. . .
. . .
</persistence-unit>
<persistence-unit name="schemaTwo">
. . .
. . .
</persistence-unit>
</persistence>
E criar um EntityManager para cada schema:
EntityManagerFactory emf = Persistence.createEntityManagerFactory("schemaOne");