nch,
From what I have read too, the smaller ones are the clones.
But propagating nurseries often use the larger "healthier looking" one, which I think is the zygote.
In your case, I believe you are using them for rootstock only....so in my opinion, it doesn't really matter too much which one you use.
On occasion, I have successfully split the ataulfo growths into 2 or more separate plants (more rootstock!), but it is somewhat trickier and not always successful depending on whether there are distinguishable separate roots for each plant/seed section.
I've got about 50-60 ataulfo rootstocks growing myself...gearing up too for the future mango scion exchange.
Good luck.