here is what I did. JBoss breaks if you try to run it in the same JVM as tomcat when using the ISAPI filters in IIS.
You must install tomcat using the isapi filter. Then run jboss (you can run it as a service) separately in a different JVM. There is a performance hit but it works well. Also you can separate your WEbserver from your application server. Unless you have a small site you will have to do this if you are using multiple-jboss's. (ie for fail over or load balancing)
In your servlet you just create a InitialContext and user a provider url to your other machine:1099 (for JNDI) and then place your jboss.jar files in the WEB-INF/lib directory (so the tomcat server can know about the HOME-remote interfaces of the EJB).
Also... if you do this you can take advantage of the getRemoteUser() method that extracts out your NT login name (if you use NT authentication under IIS setup).