If it's stable using Ntune then it's probably a good idea to set it in BIOS, otherwise you'll keep needing to reapply the settings at startup.
To get into BIOS, restart your computer. When a screen comes up that looks like this:
http://www.linuxhardware.org/images/art ... S-Post.jpgPress whatever button you need to press to 'enter setup'. On my board you tap Delete a few times, on others it's F8. Then browse to and find the settings that you've set in Ntune.
Some motherboards have an advanced section that is blocked from being accessed unless you press a special key, other motherboards have it completely blocked ( Dells).