the top bolt is for tensioning or preloading the bearing. The two bolts on the stem basicaly replace the locknut. So if your stem is on top of your stack (spacers+stem) then it should be slightly higher then your steer tube. That allows you to pre load the bearings with the stem cap bolt. Tighten the stem cap bolt just enough to take play out than tighten the two stem bolts, they are what actually locks everything in place. Theoretically after the two stem bolts are tight you could take the stem cap off which would look bad but it should not allow the stem to loosen any.