which kwami would be the "leader" of each box? (not including the duo boxes)
It's usually a second layer
Pinguu and Bloom could be considered ones, but the leaders aren't that established in the Elemental box, since most of them are second layers and Longg has a very mature personality.
Duusu is a sort of leader of the Emotion box since he's Emotion himself and has the most control over the other kwamis. Atta could also be considered a leader since she's reliable and level-headed and the kwamis listen and trust her word.
The Identity box is kinda complicated but the kwamis listen to Fluff the most. She's nice but bold in her opinions and hates the Order so that got the kwamis' favor very easily. Luppu is also a good one if he isn't grieving.
For the Movement box, probably Stikk, Pollen is too obedient and Zapp is too hyperactive.
Crassh for Potency box, Wayzz is too much of a doormat. And sure, Crassh can get very aggressive but it's better than letting everyone walk over you.
Allba usually leads the Sense box, if not him then Fleet.
Sass is actually the leader for the Timekeeper box. While Borre and Kello are second layers, Sass has more authority, he's mature and serious. Kello is right behind Sass though, he is pretty charismatic while not being silly like Borre.