Don't touch the Event Flags; you can do all of it without going in there.
Unlock editing in PokeTrainerS, then open the AR Data dialog. Add the kami (ボルトロス,トルネドス,ランドロス) to the first section of the list. Change the position of the top button to 未, THEN you can save. Do 3DS Link in-game, and all the pokemon will be downloaded from the AR Data section and placed into your active box. I recommend this method over any other.
Adding any AR pokemon triggers the first event flag in the list, with there also being individual triggers for Special Parts AR pokemon. As for the other flags, I don't know the criteria for the first one as it is not stated as an on/off trigger. The second is talking to the children when you first enter the Fertility Shrine area, and the third is whether you have received the Mirror.
Fateful is not required. PokeBox2 added a new button recently, below Ribbons, which represents the hex value for AR Pokemon. If you are going to "make" an AR kami, then use that.
Subway records.