Fig.1 shows the ATmega16A USB boot-loader circuit. Integrate all the components shown in the circuit. Download the AVR USB Flash programmer tool and upload your .HEX file on to the microcontroller. The circuit can be used as a separate programmer or it can be integrated on to your project.
Fig.1 ATmega16A USB Boot-loader circuit
Fig.2 ATmega16A/32 USB Boot-loader and Development kit circuit