Okay guys, this is a stupid question, but I want to ask it to confirm what is going on.

I took my Colt 20" HBAR up to Ben Avery this saturday, and at 50 yards with the rear sight bottomed out, I was about 6" below point of aim.  Nice tight group, just 6" low.  I had to crank the rear sight up to the 600 yard mark to level group out on target.  Since I would prefer to have a zeroed rifle with the rear sight down, I think I need to twist the front sight down more to raise the bullet impact point.  It this correct?  Also, do I need a special tool to adjust the front sight?

sorry for the stupid question, but thanks for any help.

http://old.ar15.com/books/ has the AR15 Tech Manuals.

If you download these you will locate the procedure for zeroing an AR. Rear sight is set to 300m + 1click up(I think) then you move the point of impact with the front sight shooting at 25m. I used the nose of a .223 round to depress the front detent.

For me, the tech manual procedure got me on the paper at 100yds, then I did some more tweaking of elevation (front sight) and windage (rear sight) at 100 yds.