The short answer is to first loosen the clamp bolts between the stem and the steerer tube and then adjust the bearing preload with the top cap bolt. When the bearing preload is right retightening the stem clamp holds the adjustment.
From your description I'm thinking that you might have another problem. Sometimes the top cap bottoms against the steerer tube and won't push the stem down to preload the headset. If that's the case, you can either install a small stack spacer either above or below the stem (either will work), or cut the steerer tube a little shorter.