The BIOS image saved to the HDD is accessed automatically if the BIOS becomes corrupted and you would need to do nothing. The same also applies to the Back-Up BIOS Chip (Dual BIOS).
Using QFlash you don't use the exe file. Check here for how to update your BIOS: http://forum.giga-byte.co.uk/index.php/topic,2441.0.html
This will re-write the BIOS in the Main BIOS Chip. The BIOS in the Back-up chip is not affected by flashing main BIOS and if you want to check what BIOS versions you are running then pressing the F9 key when you are at the BIOS home screen will show you.
If you want to flash the Main BIOS to the Back-up chip then you need to hold the "Alt" and "F12" keys during POST (when you first switch on the PC) You may have to try this a few times before it will work, especially if you are using a USB Keyboard.