I dont know how helpful this will be seeing its an auto, though a scrog for any photo, the screen is usually set 12 inches off the pot or there abouts. I would usually tip the plant, and if I was to do so I would set the pot centre to the screen, though seeing as we are dealing with an AF, I suggest bending the whole plant. With this method you dont want to set the pot dead centre of the screen. The best way I can explain the placement of the pot is to imagine drawing a diagonal line across the screen, that is the path you want to send the main stem of the plant, so you will want to place your pot off centre towards a corner of the screen. Dont jam it totally in the corner of the screen though, as you will want some room to train the lower branches. A screen all but negates popcorn.
From what I understand you will have some plants scrogged and others not. You may want to fix your lights at maximum height, setting the screen 4 odd inches lower than your preferred distance, because if you can do it well they shouldnt reach much higher through it. That will mean that you may have to pack up the pot heights of not only the scrogged plant but everything in the kit, so you can remove packers as the others grow....
Other than that, there may be a few other issuses for an AF that you wouldnt have with a photo. Most photos you would all but strip bare anything below the screen to open up airflow, I dont know how an auto would take to that though. Your best bet would be to get a small oscillating fan running full time and cross your fingers.
Hope that helps you get your head around it a little..... It takes a little work, and you have to be on it daily up until the 2nd week of flowering or so, but satisfaction of getting it right and a full canopy is well worth the effort.