Identify the spacers around the steerer tube, above and below the stem. Transfer some of the spacers from above the stem to below the stem. Lots of demos on Youtube , this one is good.
You can also flip the stem upsidedown.
The bolt on top of the stem cap is used to adjust downward pressure on the bearings, it needs careful adjustment. The two bolts on the stem are tightened to hold the whole steering assembly, with the correct bearing adjustment, in place. Do NOT crank down on the top bolt to tighten the stem. Once the 2 stem bolts are tightened, you can, in theory, remove the top bolt and ride without it, ie it is for adjustment only. In practice, you just leave it at the correct adjustment.
If you are not sure of the correct tightness (torque) for the various bolts, take it back to the bike shop where you bought it and let them do it.