Do the calculation of the sight height over the bore centerline at the location of the sight installation. (50% of barrel thickness at that location is the bore centerline.) Then measure the height above the barrel flat for the front and rear sights. If you make the front and rear sight heights over the centerline the same, you will be on paper, though hitting slightly low. Probably in the white but slightly low and close to the bottom of the black in a standard 8 MOA round black bull target. If you want to be conservative, make the front sight slightly higher to start with, as, you can always file more off.
I would start my sight-in procedure at a point blank range, like 25 yards rather than adding the variable of bullet drop at longer ranges. You can go there later.
Leave them that way until you develop your desired purpose load (could be a hunting load or a target load). L-R you can knock around some but filing the height is something to pretty much leave alone until that load is found. The calculation on how much to file off to raise the bullet "X number of inches" is a simple one, and depends on your gun's sight radius. Doing the math and measuring first will save you a lot of powder and time on the range in finding the ACTUAL height that works with your gun and load.
When it comes to filing your sights, you will make things easier on yourself if you measure, file 10 strokes, and then measure again. That will give you a number on how much metal you remove with each stroke, which is helpful as well. That way you'll have a good estimated number of how many strokes it takes to remove say 0.005" from your front sight. It's not exact, but it's closer to exact than guessing is. Just remember, the longer your sight radius, the more your sights have to change to affect your change in POI.