To save or create a new configuration you can proceed this way:

When all your configuration has been modified (markers name, segments, analog channels, model outputs…) you can decided to save this configuration
To do so, select New configuration from the Model Pane by clicking on the gear .
From the New Model configuration window you can save your actual configuration
The new configuration will be applied to other loaded acquisition by selecting it from the drop-down menu or by using the Startup option in the preferences.