Can someone please explain to me again the method for propagating polyembryonic mango seedlings?

Polyembryonic means you get more than one seedling from one seed. Also, the resulting fruit is true to seed.

You have to retain one seedling and sacrifice the others. But I forgot, do you sacrifice the biggest or the smallest seedling?

Polyembryonic are good for rootstocks, becuase as they are true to type(clonal) all the rootstocks should perform similarly.
Variable seedling rootstocks could perform differently, in the same soil type, climate, scion compatability etc. This gives uneven trees in the same orchard.
This may not apply to the home gardner with single trees, or pot specimens.
But known rootstocks may be easier to use.
To get a good set of say 100 rootstocks, it is better to grow 100+ seeds, and retain the most vigorous sprout from the poly seed. If you used all the sprouts from less seed, your rootstock sizes will be uneven for grafting purposes.
I'm not sure if the smaller seed sprouts have some chance of being not true to type? Apart from that you dont have to discard the other sprouts, but they seem to be slower growers when potted up.

These are Ataulfo seedlings. I intend to keep them in pots. I know they will take years to fruit but I am mainly growing them for the fun of doing it and also if I should happen to come across a scion, I'll have a rootstock. I intend to keep one to grow to maturity and another two to use as possible rootstock. Again, its all for fun.

Can these seedlings be separated? What's the best way to proceed with these seedlings? Discard the smaller ones?