There is nothing special that needs to be done. Just make sure when you bootstrap the MOXy JAXBContext that you bring in both external mapping documents. See below for an example:
package forum10874711;
import java.util.*;
import javax.xml.bind.*;
import org.eclipse.persistence.jaxb.JAXBContextFactory;
import forum10874711.b.B;
public class Demo2 {
public static void main(String[] args) throws Exception {
Map<String, Object> properties = new HashMap<String, Object>(1);
List<String> metadata = new ArrayList<String>(2);
metadata.add("forum10874711/a/binding2.xml");
metadata.add("forum10874711/b/binding2.xml");
properties.put(JAXBContextFactory.ECLIPSELINK_OXM_XML_KEY, metadata);
JAXBContext jc = JAXBContext.newInstance(new Class[] {B.class}, properties);
}
}
Note:
The above code was taken from my answer to one of your other questions (that includes a full example):