In your example, the save function will use the normal save because the "file" was not opened with your filesystem. You have to add a specific "Save file as" menu. If you open a file with your Plug-In, the application will know this, and File > Save will call your DirectFileSave function.
It's just as with the FTP Plug-In, this adds the following two menu's:
FTP File Open...
FTP File Save...
and in addition, if a file was opened with FTP File Open, the normal save function will save it through FTP as well.