Let's lay this out.
Ok, I have a Leupold target scope. Lets use that as an example. Scopes have adjustible knobs to adjust where your bullet hits. I know that my scope adjusts 1/4" at 100 yards for everytime I hear and watch it click. Now, I shoot at 3/4" target pasters at 100 yards. If my first shot is say 2 inches down and 3 inches left, I need to adjust my crosshairs. Not the scope, the crosshairs. I know that 2 inches down is 8 clicks. So I am currently hitting 2 inches low. I would move my target knob up 8 clicks. Then I know my bullet is hitting 3 inches left. I would move my target knob 12 clicks right. What this does is change the point of impact to where I want it. When you move the knob to the left, it changes the point of impact left. On quality scopes, you know when you move it so many clicks, it is going to move it exactly that number of inches. When I sight in, I know about how far I need to adjust and then I adjust it the way I need it to go. I move the bullet hole to the point on the target I want it to hit. Does that make sense? I move the bullet hole to where I want to shoot. I don't move my crosshair.
The two shot zero makes sense if you can hold the gun still and move your adjustment knob at the same time. In that case, you hold the gun still and then move your crosshairs to your bullet hole. In that case you would have to adjust the scope the opposite way of what you normally would think.
I personally just like to move the knobs the direction I want the bullet to go. If I want the bullet to move left to the 3/4" paster, I move the knob left. I think the best thing to do is just go out and do it. Take plenty of ammo and you will find the best way for you.