Generally software is only used for OC when the BIOS doesn't have the options one needs, or when doing suicide runs that might not make it to the OS as the speeds on is shooting for.
Most OCing software will have an option to load settings at startup, and without this setting you'll lose the OC next reboot.
...rightful liberty is unobstructed action according to our will within limits drawn around us by the equal rights of others. I do not add 'within the limits of the law,' because law is often but the tyrant's will, and always so when it violates the right of an individual. -- Thomas Jefferson