If it's just a flash hider just torque it down where you want it. Just like the old "A1" hiders, it didn't really matter but since it's your rifle, whatever looks best for you. Some folks don't like a jet of gas shooting straight up in the sight picture others didn't mind it.
If it's a comp, the top most, or center, port should be TDC, or top dead center. Looking over the barrel, the very center of that port should be no more than the width of the front sight post to the left or to the right.