Only one of the EJB containers is used, I think its the "Standard CMP 2.x EntityBean" one. You can configure on a per EJB basis, in the jboss.xml file, different EJB container specifications, whole or part of one. The details of this are explained in the for pay Admin Guide for 3.0. But it. You will probabvly find the answers to your other questions there, as well.
I read the paid document. I am not sure about the relationship between JRMPInvoker and org.jboss.proxy.ejb.ProxyFactory. Why the previous one is defined in jboss-service.xml and latter is defined in standardjboss.xml? Has the RMIObject port to be the same in both xml files?