I try to set my sight so the tops of both sights are the same height from the center-line of the bore. On a swamped barrel, moving the front sight away from the muzzle will lower the sight, moving the rear towards the breech will raise it. Make a mark on the center of a side flat, set the sights on top of the barrel and measure, taking account for any difference in the sight base height and what it will be after fit into the dovetail. I try to work that out before cutting any dovetails. Seems to help a great deal.
Good luck Stan!
Curtis