Well ... the story goes that it's the gods who grant your wish once you're done folding the last crane. But I don't really think it matters when exactly you decide ... just as long as you finish the folding.

[which gods, though, she doesn't specify. Madoka never really thought about the practice of folding paper cranes much — it never occurred to her before now that there would be so many other worlds, and all with their own mythos.]

Maybe part of the act of making them is to give you time to reflect — to think about what it is you really, truly want.