As Bob told me years ago, at first you have to think about it and then after awhile it becomes second nature as the system grooves in.
The way Hill explained it, the whole system is doing consciously what your eye/hand coordination uses naturally. the difference is making a conscious choice at the beginning of the the shot. I would say that to start it may very well be helpful to consciously place the point on an imaginary spot. Ferguson used stickers to place his arrow to groove in his secondary, as i seen on one of his videos. Hill also said once that one should not get so fundamental on this. As John Schulz said he never actually taught it in a step by step procedure to him. I like John's term 'conditioned instinct'. For example, if you know exactly what your point on distance is, that is basically secondary aiming, anything shorter than that of course your arrow will be lower in the field of view. Do not look at the arrow, for me it is quite a distance from the mark. For me with my middle finger just past the corner of my mouth the arrow point on deer tends to be even with their hooves. On flat ground it stays there for a range of distances, not until it gets back a ways the the point need to be higher up. but like I said, if I get too fundamental and mechanical on a live target, because of subtle position changes and the fact that game does not hold still like a target, I consider the secondary gets me in the the same zip code, but the 'conditioned instinct' fines tunes the shot to get it to the vitals.