I've seen alot of people saying stuff like: "Why didn't Discord just fiddle with Twilight from the start, instead of letting her go after the elements first? He did it on Fluttershy!" Here's my theory. And it becomes entirely clear after episode 2, so i'll put it in spoiler tags for now. (since not everyone's seen it yet) Spoiler So, first we notice Discord going after applejack. You'll notice he was trying to get her to avoid the truth by showing her something so horrible she couldn't accept it, and started accepting lies. Only THEN could Discord change Applejack's behaviour. He could only change Rarity AFTER she was tempted to go after Tom. (giggle) I could give examples on the others, but you get the point, right? Fluttershy was different. Her kindness couldn't be broken by Discord. However, Fluttershy's weakness was in fact weakness itself, so his magic could change her more easily. The phrase "Nice guys finish last." comes to mind. This is why he couldn't change Twilight from the start. Her Magic element got it's strength from friendship, which had to be fully broken first. That still leaves the question: How did Celestia know she had to send those letters? And did she know she was abusing Spike? (new Trollestia meme!) :Trollestia:
She may well have seen the end result of the girls' run through the garden maze. After all, it was visible from the tower where Celestia kept the Elements. She may well even have felt the failed use of the Elements. Celestia is basically a God-Tier Unicorn, after all, her magical senses would need to be pretty sharp.