See the instructions above. If you run into a problem then you have have to manually copy the .ftpquota file to AutoRestore Backup.
http://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/
Exception: Handling Files With No File Extensions – If you have files that are not named with a file extension then in some cases these files will not be backed up using the Backup Files buttons (in most cases files without file extensions will be backed up by clicking the ARQ Backup Files buttons). If these files are dynamically updated and are being quarantined on a regular basis and you want to exclude them from being checked by the ARQ Cron then you will need to manually copy the files to the relative autorestore backup folder path. Example: A Root file named “no-file-extension” would need to be manually copied to the relative backup folder path of /wp-content/bps-backup/autorestore/root-files/no-file-extension. You can then use the Add / Exclude Static Files tool to exclude this file from being checked by ARQ. See the example below for excluding an individual file from being checked by ARQ.