An excellent question, my dear Jazz! :D
But in order to properly answer that question, another must be presented: Why seek procreation in the first place? And the simple answer (and I stress the word simple, in comparison to the much longer version) is that 9 wanted to atone not only for his own mistakes, but for the mistakes of the Scientist. He felt the weight of a dead world on his shoulders and sought to correct it.
To that end, 9 became something of an alchemist. And through the extensive knowledge he gained, he, 7 and The Twins were able to crack some of the Talisman’s secrets. Thus, the first method came into play…
By dropping soul-water into the Talisman’s inner matrix, new souls were created, and new stitchpunks by extension. These stitchpunks were crafted as what would be equivalent to an adolescent and would generally come to be regarded as “pure-forms” by future generations. Eventually, many of them would become the first members of the Scion Council (alt. “Council of First Children”) and would continue to create more stitchpunks in their image.
Now, a problem arose with this creation method: at some point, it just stopped working. At the time it couldn’t be known whether this was because the Talisman would no longer accept the soul-water, or because the water had somehow gone “sterile”. But they needed to find a new way to procreate, and thus the method of “bonding” was devised — which is all at once exactly what it sounds like and not what it sounds like at all. xD
Bonding allowed stitchpunks to reproduce among themselves, without the aid of the Talisman — carrying and nurturing the souls within themselves before transferring them to a new body. But this method didn’t come without consequence: stitchpunk lifespans were significantly shortened, and the souls and bodies containing them needed to begin at an “infant stage” and grow by way of regular augmentations. Despite this, many were content, and bonding has continued to be used until the present story. Naturally, love among stitchpunks also became a more widely accepted ideal thanks to this.
But don’t be fooled: With the rise of stitchpunk alchemists, many tried and failed to create a synthetic version of the original soul-water in the hopes of recreating the initial generation’s “purity” and do away with bonding altogether, as some were uncomfortable with the idea of blurring the line that separates them from man.
This, however, created only abominations…
…Oh gosh, I’m sorry. xD I got waaaay off-track there. But I do hope that’s a satisfying answer, for now~ <3