All container setup, such as ports to listen on, webapps to deploy, thread pools, security etc is done in a jetty configuration file in xml format. An example of such a file is provided in the distribution as etc/jetty.xml. For more information on this file, see the FAQ entry What is jetty.xml?
Additional configuration can be performed on a per webapp basis in a file called jetty-web.xml file placed inside the WEB-INF directory of the webapp. See also What is jetty-web.xml?