Use "Apply at windows startup" and see if that works.
Also, use MSI Afterburner or a program that allows you to set profiles, for example, profile 1(no overclock) for 2D clocks and profile 2(oc'ed - or not) for 3D clocks.
To do that on Afterburner, adjust the clocks click save and store it. Then go to settings -> profiles and set the 3D profile to the one you saved earlier. That way each time you launch a 3D application that profile will load and the clocks should be stable.
By adjusting the clocks you mean to manualy downclock? Like the opposite of overclocking? WHat I want is that when I game I always have the 3d clocks, I don't want to have 2d clocks, I believe that's what you treid to tell me but I got a little confused.