The iPlanet web server typically installs under /usr/netscape/server4
The default web directory is /usr/netscape/server4/docs which is equivalent to "tomcat/webapps/mydirectory "
As long as the lib jars and the classes directory is in your server classpath, it shouldnt matter where you create them.
The iPlanet administration tool will be running at http://localhost:8888
(unless you specified a different port during the install). There you can specify the server's classpath, as well as other configuration settings.
Hope this helps