Our Intranet is stored on a File Server.
The only two things I've generally kept in mind is that you point IIS to the correct location of your site, whether it be locally or on a network drive. Secondly, when you create a new web, again make sure you specify the correct location. As long as FrontPage is allowed to apply it's necessary features to the folder it can reside anywhere on your network.
All FrontPage's features should then work for you.
Craig