Hi Benny, I am happy to hear that your are enjoying Total Upkeep so far!
The FTP remote storage settings for our WordPress backup plugin has a field in there titled Folder Name and you can configure a unique folder for each of your websites to use for backup storage. You can locate the FTP storage settings by navigating to Total Upkeep > Settings > Backup Storage in your WordPress dashboard and then click the Configure/Update link next to the FTP/SFTP option. The Folder Name field is just below FTP Username and FTP Password.
Please let us know if you have any other questions for us Benny!