Documents (sometimes referenced as resources, because there are plans for the future) are organized into projects. You may open and edit multiple documents at once using tabbed panes. Documents are organized into projects.
Projects represents hierarchical structure of documents and folders. Projects are identified using unique URL address. Amy Editor can open any project available at any URL and it can have any number of projects opened at the same time. They are visible in the left accordion pane of the editor. In order to start working with documents, you must know a project URL. Project URL is a simple HTTP address, pretty much the same as an address of a website. 
Once you type the project URL into the "Open project…" dialog field, the address is checked and displays project information together with the "Open project" button for opening. The checking is done on-the-fly as you type the address. Now, some projects requires additional parameters to be specified (such as username, password etc.). If this is the case for the project you're about to open, you will be prompted to fill these parameters as well. Once properly filled, you hit the "Open project" button and project opens. 
You will see classical tree-based view of the project hierarchy. 
Clicking on any document will cause loading and subsequently opening the document in the editor.
There are basically two types of projects. Default projects and projects anyone can define for their own purposes. Appart from URL, projects may require additional parameters, and can be marked for read-only or read/write. You will always be notified, before opening project, what parameters and editing type the project is.
Default projects include support for well-known protocols such as FTP, WebDAV and Blog API. In practice this means, in Amy you can access and modify any documents on any FTP, WebDAV server where you have access to. Directly. There is an experimental version of SFTP (FTP over SSH) access too. Blog APIs even allow you use Amy Editor as your editor of blogposts on your blog. For those of you, who just want to try Amy for the first time, without knowing anything about projects, there's always possibility of opening default publicly shared project called Playground.
There might be (and probably are) reasons why you cannot live with default projects. Either you don't want to access documents via FTP, WebDAV, or you want to limit access more precisely. Or you just use something else. For those of you, there's an API and libraries in various server-side languages (PHP, Ruby on Rails) that you may implement and create your own project at specific URL. With its own hierarchy, document contents, access rights etc. Details of implementation are more deeply covered in For Developers section of the Amy Editor website.