You can refer the section 8.1.1 of the attached document. http://www.cypress.com/file/139296/download
FX3 has the option to boot from SPI/I2C which you can use if you want the FX3 to boot directly with your firmware (bootloader will not pop-up). For this you need to have a SPI Flash or a I2C EEPROM connect with to the FX3, and the PMODE pins should be set to boot accordingly (refer datasheet to see PMODE settings). You can use the same .img which you use for RAM download in section 8.1.1, and program by selecting SPI FLASH/ I2C EEPROM in the section 8.1.2
I get an "access denied" message when accessing that file.