JBossWS is about portable J2EE compatible web services. Your client code should not be dealing with Axis serializers/derserializers.
The XML/Java mapping should be defined in jaxrpc-mapping.xml which can be generated using wscompile.
If you need more control, have a look at ws4ee-deployment.xml, which is described on the wiki.
No, you cannot have any other axis version than the one jboss provides. That JBossWS still uses axis is an inmplementation detail that will be removed in future.