You have a FileMaker database, hosted on FileMaker Server. Separately you have a file you're modifying locally in Pro that is going to be your "sync" file. It will connect to the FileMaker Server box via RESTfmSync for this operation. Once the modifications are complete you can distribute this file on Pro or Go for end users to utilise.
Although it's possible for the server and local files to be the same file, all of the documentation will assume that they're separate, and will refer to the "Server File" and the "Local File" separately. The setup described in this documentation assumes that all changes to the data are done on the Local File while the Server File is just a set of passive tables used as a central repository.