When you have build your documentation you will probaly want to save the settings. All you do is to save your project. The project is saved in a .orp (ORtelius Project) file. The next time you start Ortelius it will automaticly open your recent project.

If you work with different project, you just save each project in its own file. You can open the project from Ortelius or by clicking on the .orp file. You can also work with multiple instances of Ortelius at the same time.