The following two links will help you understand the serial protocol and how the pins are used with and without HW or SW handshaking. I recommend that you read them both thoroughly:
http://digital.ni.com/public.nsf/websearch/2ad81b9060162e708625678c006dfc62
http://digital.ni.com/public.nsf/websearch/e22da85e97818de78625678c0069bfc9?OpenDocument
Best Regards,
JLS