The server-side scan is an extension to our remote malware/blacklist scan and it runs once per day.
Enabling is very easy, just follow these steps.
Server Side Scan File
The Sucuri scan file must be located in your root web directory. The scan file is uploaded to your site root web directory, using the monitor S/FTP interface or your S/FTP, SSH or cPanel.
Once uploaded, the scan file will be accessed by the monitor server using curl over ports 80/443.
If you need to reupload your server-side scan file go to your site Monitoring Overview -> Settings -> Server Side Scanner to download a copy.
Temporary Scan File
You might notice that during scanning a temporary file is created in your root web directory. The file will be called sucuri-sss-resume-(LONGSTRING).php The server-side scan resume feature was recently implemented to help overcome host server resource limitations.
If you are still not sure what do, please feel free to open a support ticket with the Sucuri team.