DS2411P is an unique serial number generator. As this design is that of Xilinx, a thrid party, I recommend you to contact them for details.
You will need to use the GPIF interface on Fx2LP chip to interface to external processors for data transfers.
Please refer to this AN to understand details of this: http://www.cypress.com/documentation/application-notes/an66806-getting-started-ez-usb-fx2lp-gpif
Once you have understood this, you can create a tech support case on our website to get your schematic design reviewed.