Your data in Logos is stored in entries, which can be assigned to projects. You can link each entry to one or several projects.
For instance, you can have course notes about Rousseau filed under the 'Rousseau' project as well as under the 'Intro to Political Science' project.
You can also have a quick shopping list, for instance, that's not assigned to any project.
Projects can also be grouped by class. Classes help you sort your project list. Examples of classes are 'courses', 'personal', 'work' etc. A project belongs to a single class.
The buttons and navigation should be self-explanatory. In order to assign an entry to a project, just go to the entry and click the projects text box.