Depends. But, using the example of the Brother MFP since it is the #1 MFP/MFC with users at least on the board, you would connect it to the network, then in settings you would set up the path you wanted the fax to go.
I don't know the Brother very well, but if you were using Muratec or Xerox or HP which had fax servers in them, you would connect them to the network, and either use the walk-up screen on the MFP or just log into using your web browser, and set the path to any folder you wish. Usually a shared folder on your server.
To fax from your PC, you would need software. If the fax server is contained in an MFP or other Fax machine, it will likely provide you with that software.
It is rather simple, and the company you purchase it from can set it up for you.