The CodeGuard application is built with single sites in mind, but there are several options that would work when it comes to WordPress Multisite.
The first approach is to back up all of your sites from your main FTP account, effectively treating your multisite as one large website. In our initial activation process, we let the user choose which files on their account that they want to backup. Here you could select the main folder for each of the sites that are on your network. Each time a backup is run, all of these sites will be backed up. For restoring a site, you can use our selective restore feature so that not all of the sites on your network get rolled back. You can add the database to this account as well.
Your other option would be to create separate FTP user accounts for each site with the FTP root being the root of the specific website. This way all of the sites would be backed up and restored independently of one another. For the database, you can back that up under your primary account.
If you have any questions about this, please feel free to reach out to our fast and friendly support team.