Of COURSE your 3dMark06 score isnt going to go up by much. At the end, when you get your score, click 'advanced' or something to bring up a breakdown of the score. 2 of the tests will be GPU-heavy, and will make up most of the score. One test will be CPU-heavy, but will contribute little to the overall score.
When you run 3DMark, breakdown the scores so you can see what tests your overclock is improving.
Or, just run SuperPi, 1mil. Quickest way to see the improvement you're getting.