TE0320 comes with FX2 USB microcontroller's firmware.
The modules shipped before 2/09/2013 comes with Generation 2 firmware.
The modules shipped after 2/09/2013 comes with Generation 3 firmware.
To change the firmware of EEPROM from generation 2 to Generation 3 you must follow this procedure. You may also watch this video play list.
Those preloaded firmware is used with TE API ... .
TE0320 comes with SPI Flash preloaded with a reference design?
Those preloaded image is just for getting started demo, for real designs:
Cypress tools (....) or Trenz Electronic Tools (...) can be used to load FX2 USB microcontroller's firmware.
Xilinx Impact can be used to load bitstreams.
Xilinx Impact can be used to load bitstreams.