On the master machine:
In Automator create a new workflow where step one is Get Specified Finder Items from the Finder library, and select the bookmarks.plist file which can be found in ~/Library/Safari. Then add the Upload Files action from the Transmit library. Enter the FTP server, upload path, and select replace. Save the workflow as an application.
On the slave machine:
In Automator, create a new workflow where step one is Download Files from the Transmit library. Set the FTP server (in Transmit, you should create a favorite that automatically logs in and changes the local path to ~/Library/Safari. Save this workflow as an application.
Now when you run the upload application, it will upload your Safari bookmarks to the FTP server. When you run the download application on the other machine, it will download the bookmarks.plist file from the FTP server and replace your local copy. For safety's sake, I have the download application set to ask before it replaces my local bookmarks file.

