I am assuming you are running Tomcat under JBoss. If this is the case you would simple place your WAR file in the JBOSS_HOME/server/<server-config>/deploy directory where <server-config> is the name of the server you are using. The default server started with run.sh is simple 'default'
With WAR files, utility JAR files that are needed by your Web classes should go inside the WAR file the structure should look something like:
The WebApplication loader will automatically add classes from the WEB-INF/lib directory to the CLASSPATH.