Upon starting Kodo Workbench, a welcome dialog will appear and allow you to enter your license key, as well as the working directory for the workbench. By default, the workbench will be configured to use the pure-Java Hypersonic database, which allows you to experiment with Kodo without having to set up your database. You can always change these settings using the Pereferences and Kodo Configuration menu items.
Note that while Kodo Workbench will remember your file settings, it will not attempt to remember the contents of those files. This means that if you change the file, on future restarts, Kodo Workbench will follow the changed settings of that file.