The navigator tree is the panel on the left, which allows you to navigate between the documentation, your databases and the tables and items stored within those databases.
The data that you ReQord will be stored inside the databases that you create. With the navigator tree you can select these items, some of which will present you with more options in the options panel.
Note that the properties file is also a database, if no such file exists you will be given the option to create a new one or import an existing one. All your preferences and watchlists are stored inside the properties database, so if you create a new one you'll reset all those values to default. The properties file is also used to remotely connect with a ReQorder session on another machine.