If I understand correctly, you have a standalone Remoting application that you want to integrate into the Application Server. The main thing you would need to understand is how to tell the AS to start the server side of your Remoting application. This is done by way of configuration files. There are a couple of places you should look for more infomation:
1) Section 126.96.36.199. "Declarative configuration" of the Remoting Guide (http://labs.jboss.com/jbossremoting/docs/guide/index.html) describes Connector configuration in XML files.
2) If you look at the jboss-service.xml file in the server/default/conf directory of an AS installation, you can see an example. In particular, look for the configuration of the "jboss.remoting:service=Connector,transport=socket" MBean.
3) For background information about MBeans, see the The JBoss 4 Application Server Guide (http://docs.jboss.org/jbossas/jboss4guide/r5/html/).
4) If you're using the http transport, you might want to take a look at the servlet transport, which uses tomcat in the Application Server. See Section 5.4.11. "Servlet Invoker" in the Remoting Guide.