Ok with that into I will take it.
I would say zero (at 50yards) with whatever aperture you use the most often - as the holes in the A2 apertures are at different heights.
Forget about using the A1 aperture it doesn't get you anything.
I zero my A2 aperture equipped ARMS #40 (virtual A1 sights) at 50 yards with the large aperture as this is the one I use most often. The small aperture will have a zero in the 300M range due to the offset.
If you zero with the small aperture at 50 yards you have a great chance of the large aperture never 'zeroing' with the round - you will always have an offset with the offset getting larger as you go downrange.
On my A1 uppered M4 I use the Ashley same plane rear aperture (similar design to the A2 but the holes are slightly larger). Both big and small holes are on the same plane so you don't change the zero when you flip between them. For this aperture always zero with the small hole.