The manager.properties file located in the system subfolder configures the JSM instance. It controls the TCP ports used, tracing, secure socket layers and many other important properties of the JSM execution.
The manager.properties file is loaded when the JSM starts. If the manager properties change, you can reload the new changes by using Studio Refresh option (described in 2.6 Java Service Manager Refresh). See Some changes, such as TCP ports, would require a reboot of the JSM instance for the changes to take effect.