The EEPROM can be read or written using vendor commands unique to the CY7C65640B/30/20. These vendor commands are in the data sheet and can be used by any programs configured with them. The reference design does supply a program which allows the writing or reading of the EEPROM. Please see the web page www.cypress.com and select reference designs for USB hubs and you will find a copy of the program.
If you program the parts using a separate EEPROM programmer, please inquire with the EEPROM programmer's vendor for further information on how to program the EEPROMs.