The automated backup found in the admin section set for certain days of the week does a full backup of each course. You can set it to backup all content and user data if you like. The resultant zip files for each course will be saved in the backup folder of each course. You can tell it on the same screen to save them all in a designated folder, which is a good way of ensuring they are easy to locate and indeed the folder can then be backed up to tape or alternative server.
This backup I call "automated course backups".
Other backups include:
- site backup - where you use a tool like rsync to backup moodledata folder and do a dump of the database
- manual course backup - which is what you describe you do inside each individual course, click on the backup link and perform a one-off backup of that course
Jason