by Pedro Castro » 18 Jul 2013, 17:35
Xboard protocol version 2 has "setboard" command. You must use a GUI like Arena or Winboard to configure the position and GUI send this position to engine in FEN format if engine supports the setboard command.
Some engines will have an option to set a position from the console, but most do not.
It is engine who understands the FEN format, not the protocol.
Best wishes,
Pedro Castro