One of the screwy things to wrap your head around when you use scopes....
When you adjust your scope turret "up", it moves the cross hairs down, which causes you to raise the bore to hit higher. Makes sense ?
If you rotate the turret "down" it raises the crosshairs causing you to lower the barrel and hit lower.
A 20 MOA rail should tilt the scope down 20 min, thereby raising the bore by 20min when the scope is horizontal (which is how you get the "extra" 20 min of elevation for long range). So, with the scope centered and sitting on a 20min rail and the barrel pointed at the target, the scope should be pointing below the target at close range. If you point the scope at the target, you should be hitting 20 min high. Therefore after fitting the scope, you would expect to dial the turret "down" 20 min to compensate for the rail tilt. At this point you should be at the same point you would be at if you installed a scope on a "flat" rail.
Now sight in as normal.
If, when you did the boresight, the scope was pointed above the target, it suggests the scope rail was reversed and pointing upwards instead of downwards. You should still have been able to zero it, but then you would only have 17min of elevation left which is not very useful.
Once you have your scope zeroed, you can forget this for a while. Then up, down, left and right move the point of impact in those directions.