You put the best treasure tools, equipment (refined / charmed), charms, magatamas and rune stones on your position 1.

This is really more mid and late game. It means, that you have magatama / runes lvls 1-2 levels above your other ninjas, before you upgrade them. Ofc you still want a strong team...so you do not just charm him to 3 slots and give the other ones no slots. It means, that first you open up the rainbow-magatama slots on your main, then on your others, then you give him the second spot (on every position) *ways put the best (highest level magatama) on him.