ATI Tool cannot work with 2D/3D clocks natively yet. What you have to do to use it is disable the ATI poller services * these are what the ATI driver uses to change between 2D and 3D clocks* and OC in 2d mode. After that, open ATI tool and ramp up your "2d" voltages and clocks to appropriate levels for 3D * check
here for examples*
Once you have your highest possible/desired OC, you can even set up different profiles, save your "OC" as one, then save the default 2d as another. Further, you can tell ATI tool to load the "2d" profile at startup, then load "OC" whenever you start a 3d game.
Missing Nvidia coolbits yet ?
I am going to suggust something that isnt too popular here.. Load 6.3 cats and Cat Control Center ( CCC ), select "Advanced" view and go into the Overdrive tab. Do your O/C ing here, chances are you will be able to hit the wall before you reach the maximum OC from the overdrive panel. At least that was the case for me on stock cooling, I didnt need ATI tool till I went to water, but YMMV.
If you can max out there then look to the other solutions, or just call it good enough.