The conf/jboss-service.xml file is described here. There are relatively few things that can be done to the naming service, mainly you'll change the port or bind address. As with all changes to conf/jboss-service.xml, you will need to restart JBoss for them to take effect. If you wish to make runtime changes you should use the JMXConsole. Instructions for configuring the naming service via the JMXConsole can be found here.
Open the conf/jboss-service.xml in vi or some text editor capable of saving in plain text. Scroll near the bottom to the MBean definition for the naming service:
<mbean code="org.jboss.naming.NamingService" name="jboss:service=Naming">
Looking a bit lower you'll see the port that the JNDI naming service is listening on. If you change this you will need to change the JNDIClientConfiguration as well:
<mbean code="org.jboss.naming.NamingService" name="jboss:service=Naming"> <!-- The listening port for the bootstrap JNP service. Set this to -1 to run the NamingService without the JNP invoker listening port. --> <attribute name="Port">1099</attribute> <!-- The bootstrap JNP server bind address. This also sets the default RMI service bind address. Empty == all addresses --> <attribute name="BindAddress"></attribute> <!-- The port of the RMI naming service, 0 == anonymous --> <attribute name="RmiPort">1098</attribute> <!-- The RMI service bind address. Empty == all addresses --> <attribute name="RmiBindAddress"></attribute> </mbean>