The AutoRestore Read Me help button text below needs to be changed/updated. This particular help text was originally created years ago and for older versions of BPS Pro. So yes you should always try to use the AutoRestore built-in tools to do things instead of doing them manually, but if you do have to do things manually then the worst case scenario is that files would be autorestored and/or quarantined and you would just have to restore those files from Quarantine. Disregard this help text “this could result in serious website problems” because that is no longer true anymore. This help text will be changed/updated to in the next BPS Pro version.
ARQ includes all the tools you will need to perform any action you need – backing up files to backup, deleting files from backup, adding additional website files and excluding files from being checked by the ARQ Cron. You should NEVER manually (FTP or Web Host Control Panel) change, modify, move, upload or delete any files in backup. ARQ is utilizing your database to perform some tasks so if you manually (FTP or Web Host Control Panel) change any files in backup then this could result in serious website problems. All the tools you need are included in ARQ and you should not have to do anything manually with backup files.