I don't understand the question. You wonder what takes priority with virus protection? I would hope that you would protect the server first if that is where everybody stores their data. Basically, the virus scanner is designed to protect the computer in which it is installed. You can download files from the server safely (for the most part) if the virus scanner is updated as it should be. However, users can still download infected files from the Internet and mess up their own systems. Personally, I would protect the server because if your server gets infected, the virus can migrate to all of the clients. If one of your clients is infected, the virus will probably be stopped once it reaches the server (depending on the topology you have set up).