After 10 years working with EA I found the most important setting the "Set as Namespace Root" in the Project Browser.
This way you can direct the import of classes and their namespaces into different packages e.g. for different libraries.
I ended up creating different root base packages (e.g. model, application,
libraryX) and import the classes from their base folder into those packages.
Check the by namespace toggle instead of by folder toggle for Java. You can also select to create a diagram per package during import. The same process works very similar to import a database schema from a DB.
Once you have imported all relevant classes (and libs) you can arrange them on new diagrams as you require. Sequence/ Diagrams to show behavior, or class diagrams to describe related objects. I think the real power of EA lies in connecting design elements with code elements in the various model views.