Before copying your files to FileMaker Pro, it's a good idea to open your site folder in the Site Editor and perform media consolidation and verification of links and references. See chapter 12, Uploading your pages to a Web server for information on how to do this.
You can copy your site folder to the FileMaker Pro host computer using your network software to mount the server volume and copy your files onto it. Copy the contents of your site folder into the Web folder, which is located in the FileMaker Pro application folder.
See the FileMaker Pro documentation for more information.