Of course, the Server Edition only takes care of the server itself. I mean, it installs only on servers, and handles only the stuff that goes through the server (files, e-mails etc).
To protect individual computers on the network (at workstation level) you need to have the software deployed on all these machines - but not the Server Edition (which is designed only for servers) but the regular, workstation-based, "Professional Edition".
The upcoming 'Network Edition' will greatly simplify the deployment task, and will also provide efficient means of [remote] administration but until it's ready you can stick with the 'Server Edition + N Professional Editions' scenario.
Anyway, to answer your questions:
you'd install avast Professional on one of your machines, and then let it generate the Silent Installation package that you will in turn run on all of the remaining machines. PRGFILES refers to the system 'Program Files' directory (whatever its name is - please note that the names of these directories are localized). As about the settings, it's really up to you - I don't know if you want the process (the gauges) be visible on the screen or not (silent x very-silent) or if you want the installer to automatically initiate system reboot after completing the installation or not (if you opt not to reboot, the installation will not be complete till the next time the user reboots)...
Hope this helps,
Vlk