Hi, I'm not the creator but I hope you don't mind me answering because I remember this tripped me up early in development too, but it's surprisingly simple! Using your example, the format you'd need is this:
[["I am not crying," you say, even tempered. You want to, though!|2][$stoic = true]]
Whatever you put in that second set of brackets inside the choice will only execute when someone selects it. You can also have multiple variables in those brackets, just separate them with a comma. For instance if you wanted to like, let someone change their hair mid-game you could have something like
[["It's perfect!"|2][$hair = "straight", $hairlength = "short", $haircolor = "blue"]]