You either run regular gbak tool like

GBAK -B fbservername/portnum:<PathOfDatabaseAsServerSeesIt> <PathOfBackupOnYourLocalPC>

or you use Services API, that can also be called using -SE switch of GBAK this way

GBAK -B -SERVICE fbservername/portnum:SERVICE_MGR <PathOfBackupOnServerPC>

Ivan
http://www.volny.cz/iprenosil/interbase/