With my older eyes the rear sight is usually forward of the breech area about 12"s, and a bit forward of the balance point. I then measure the height of the notch at the top of the "U" (or "V") of the rear sight, and purposely fabricate the front sight so that it is a bit higher than that measurement. Align both so that they are centered along the barrel. The bullet impact will print a little low at 30 yards but centered within acceptable limits, I shoot a few strings without moving or filing the sights to see how it prints on target and, of course, for grouping. Once I move out to 50 yards I get serious about powder charge, but keep the same ball/patch combo, and shoot only for grouping again. Once I have a tight grouping I will normally have file a bit off the front sight to raise the impact point, and if needed move the rear sight very slightly left or right. This is how I've done every gun I've built, it works, and isn't too much of a hassle to have the gun shooting bullseyes soon enough.
In short: fabricate your front sight a bit higher than the top of the rear sight, center the sights on the barrel. Only file the front sight when you know how the gun groups.
dave