This is what I run from DOS prompt:

"C:\Program Files\Microsoft SQL Server\90\DTS\Binn\dtexec.exe" /f {dtsx_file_name} /CONNECTION DestinationConnectionOLEDB;"trusted_connection=yes;Database={db_name};Server={server_name};Provider=SQLNCLI;" /CONNECTION SourceConnectionFlatFile;"{path\flat_file}"

Replace {} with proper names.

The name of connections matches connections in SSIS...