When you save your document all project information is preserved, allowing you to edit it at a later date. The design project is saved as a single file with the extension .afdesign.
The first time you save your document, you'll be asked to give the project a name and save location. Following this, future saves will overwrite the previous version.
Optionally, you can save a current project as a new project. In this case, the new file will not overwrite the saved version.