To configure CYUSB3343 to boot from EEPROM. You just need to set Pin MODE_SEL[1:0] to 01, and connect I2C interface to EEPROM. Then the device will boot from the firmware installed in EEPROM. You can download the firmware into EEPROM by using Blaster Plus Configuration Utility in the following page:
The configuration between EEPROM & I2C uses I2C interface. It provides data transfer with only two lines( CLK& DATA).