The F-PROT Antivirus Updater requires you to have a valid licence key, typically stored in the same folder as the updates itself (example: /opt/f-prot/fpav.lic) but it can also be stored in /etc/f-prot.conf.
The virus information is stored in a file called antivir.def and it resides in the same folder. If that file does not exist when fpupdate is run it will be created. If it does exist, only an update to the file needs to be downloaded instead of the entire file, which saves considerable amount of network traffic.
To run the updater manually you only need to run the fpupdate program, assuming your licence key is valid and you have a working network connection. While the update is being downloaded you will see a percentage of how much of the download has been completed, and if all goes well nothing more should happen and the update has been applied.
The installer should normally create a cron entry that runs the updater so a normal user should not have to run the updater manually.