You can use the command line option "-ntc" to specify the configuration file for Net Time Server & Client. By default, it's NetTime.ntc and located in the installation folder of Net Time Server & Client. See also the "Command line parameters".
If a Net Time Server & Client instance already exists, and you try to launch Net Time Server & Client with the same configuration file again, then the running instance will be actived.
You can specify dissimilar configuration file in command line to create multiple Net Time Server & Client instances, if the configuration file doesn't exists, it will be created automatically with default settings.
Also you can use these instances to install multiple Net Time Server & Client services. These services will use their respective configuration files. See also the "Service".