You don't need to flash the NAND directly once everything is working. There's quite a few programs out there that do the work for you such as Freeboot Toolbox Maker:
LinkI recommend you do some research as things CAN go wrong. Here's some quick instructions I just wrote up, hope it helps you get on the right track..
-Short Instructions-
If you don't have your CPU key, boot your 360 with the EJECT button. The Xell(ous) screen should load up. Combine fuses 3&5 to get your CPU key. Triple check to make sure you write it down correctly.
Grab Flash360 from the 'usual places' - start it up from your console, backup your current nand (press X) and FTP it to your computer (it will be in the same folder that Flash360 was ran from).
Use Freeboot Toolbox Maker to prepare the updated image, follow the onscreen instructions that should be pretty self explanatory.
I recommend checking the file in 360 Flash Tool before flashing. You can download the latest version
here - (Enter your CPU key before trying to open your image - Settings > Keys) The File System tab (once the image is opened) should have a total of 29 files.
Once the image is done, rename it to "updflash.bin" and place it on a flash drive (or FTP to flash360 folder on your 360) Finally, flash with Flash360:
Button A (write updflash.bin to NAND)
Button B (Raw Flash without keeping current kv/config).
Ignore these ("WARNING: Keyvault encrypted data check mismatch" and "WARNING: Your current nand is not the ZeroPaired.").
Continue with the Start button.
Pressed A after the 2 warnings to continue with the flash.
Once it's done flashing, press:
Back
Back to Turn off Xbox 360
Shutdown timer...
Remove power cord and wait atleast a minute.
Turn it on and it should be good to go!