Save and back up projects

To save a project, choose File > Save.
To save a copy of the project with a new automatically generated name, choose File > Increment And Save, or press Ctrl+Alt+Shift+S (Windows) or Command+Option+Shift+S (Mac OS).
A copy of the current project is saved in the same folder as the original project. The name of the copy is the name of the original followed by a number. If the name of the original ends with a number, that number is increased by 1.
To save the project with a different name or to a different location, choose File > Save As.
The open project takes the new name and location; the original file remains unchanged.
To save the project as a copy in the XML project file format, choose File > Save A Copy As XML. (See About projects.)
To save a copy of the project with a different name or to a different location, choose File > Save A Copy.
The open project retains its original name and location, and a copy is created with the new settings but is not opened.
To automatically save copies of projects at regular intervals, choose Edit > Preferences > Auto-Save (Windows) or After Effects > Preferences > Auto-Save (Mac OS), and select Automatically Save Projects.
Auto-saved files are saved in the Adobe After Effects Auto-Save folder, which is located in the same folder as the original project file. Auto-saved filenames are based on the project name: After Effects adds “auto-save n” (where n is the number of the file in the auto-save series) to the end of the filename. Maximum Project Versions specifies how many versions of each project file you want to save. When the number of versions saved reaches the maximum you specify, the Auto-Save feature overwrites them starting with the oldest file.
To save a copy of the project and copies of assets used in the project to a single folder on disk, use the Collect Files command. (See Collect files in one location.)

You can’t directly save an After Effects CS4 project for use in After Effects CS3 or earlier.

Jerzy Drozda, Jr. (Maltaannon) provides instructions on his website for a manual—but still relatively efficient—way of copying data from an After Effects CS4 project into an After Effects CS3 project.