I think you already found out that if you want to use the stack that comes by default with AS6 (jbossws-cxf) you need to look at the jbossws-cxf documentation, http://community.jboss.org/wiki/JBossWS-StackCXFUserGuide .
In any case, just to clarify, the jbossws-native standard configuration files (standard-jaxws-endpoint-config.xml, etc.) currenlty live inside jbossws-native-core.jar that's in common/lib and client folders. Users are not supposed to changed them. However they can provide their own configuration embedding similar conf files in their deployment.