You can look at the Superspeed Explorer Kit schematic, The CY7C65215 not used to program the EEPROM. CY7C65215 is a USB-UART/I2C/SPI/JTAG bridge. It is provided in the kit for debugging purposes like UART or JTAG debug.
Explorer kit has an on-board EEPROM, which can be written with the desired firmware image, In this DVK, we can write the EEPROM memory by selecting the EEPROM program option in the control center. (this action will dump the FX3 with a Boot Programmer firmware, which will then write the EEPROM device through the FX3 using Vendor commands. Once the .img file is written over there, you can reset the device with PMODEs set for I2C boot.
Thank you very much. Best regards.