Within reason, it really doesn't matter, but you must shoot that exact same load every time . If you shoot one load and then another, you will never make sense of the sighting-in procedure. The load can be modified later, honed to the best you can work out, after you have the rifle shooting on the paper at distance. Look at the center of the group and decide which direction it must move to put the group on the aiming point. Now adjust the sights to put the group where it should be in relation to the aiming point.
Sights come in two main categories, adjustable and fixed.
Adjustable sights can be moved with impunity, because if you move them too far, you can simply move them back again, no sweat. Not so with fixed sights. Adjusting fixed sights for elevation involves filing away metal, which can't be put back, so you must be careful. I strongly recommend that throughout the sighting in process, you plan on making the bullets hit low on the target. The reason will become clear.