By default internal agent is configured to my understanding and the related entry is in domain.xml at path <Controller_install_dir>/appserver/glassfish/domains/domain1/config/ path like below under xml section <config name="server-config"> and the path of agent directory is <Controller_install_dir>/appserver/glassfish/domains/domain1/appagent/ and it is auto filled with config details during installation of controller itself.
Regarding no load on flow map query: We see it could be that either agent have reporting issue OR transaction config for Servlet/ EJB/ auto discovery entries are disabled, Can you check below:
1) Under Configure -> Instrumentation -> Transacion detection screen, check if "app server" tier have Servlet and EJB both entry and auto discovery checkbox section are enabled, if using new config 2.0 view, edit "java auto discovery rule" and check above entry settings and enable checkbox if not enabed in UI and see how it goes. (refer sample section we are referring in attached view)
2) If 1) does not help share agent node logs folder for our review in this post we will suggest next steps, That is attach logs folder from <Controller_install_dir>/appserver/glassfish/domains/domain1/appagent/ <ver>/logs/Node1/ path
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