You can use Folders to organize your documents in whatever collections make sense to you.
Documents can be in more than one folder. You can assign tags to each document in your Library and use these tags to help to locate and organize documents.
You can also use the star icon to mark favorite documents, and mark documents as read or unread using the green circle.
This video (from 2011) provides a good overview of how to navigate and organize your Mendeley Library:
