@ McHenry – The AutoRestore/Quarantine procedural steps for manually modifying or uploading files are below. There are tools already in AutoRestore where you can do what you are asking, but to be honest with you it is much simpler just to do the steps below.
http://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/
AutoRestore/Quarantine Correct Usage
AutoRestore/Quarantine (ARQ Infinity) IDPS is a real time file monitor that monitors all of your website files for any changes. When manually uploading files with FTP or modifying files or folders on your website follow these simple procedural steps for AutoRestore/Quarantine (ARQ) to avoid having those files autorestored and / or quarantined. If files are sent to Quarantine then use the Restore File option in Quarantine to restore those files. ARQ is amazing, but it cannot tell who you are if you are manually modifying files or folders outside of your WordPress Dashboard – that is not possible.
1. Turn ARQ Off.
2. Upload or modify files or folders on your website.
3. Click the appropriate Backup Files button: Root Files, wp-admin Files, wp-includes Files or wp-content Files Backup Files button.
4. Turn ARQ back On.