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.

sry im kind of new but can anyone explain this in a different way

Easiest I can think of, by the end game( or mid if your p2w) the resources needed to upgrade everything evenly become so high that its best to focus on one important ninja first, trying to get close to cap before investing in the others. You take a set of tools with the best purify rolls and focus on getting them to the best they can be, generally this after getting all your gear to refine 6 or 7 and charm 6. From there you push the charms and refines to lvl 8 or above, the rune stones to lvl 10+ and magatama to lvl 8+, and equip your desired ninja with the tools and put him in first position. If everything has gone well than you should have a ninja with about 10k+ more bp and able to get there mystery off before everyone else. Do note, this only becomes "mandatory" once you begin crossing the 90k total team bp range.

TLDR: S*** expensive so put your nice stuff on your show star

Examples of common position 1s: Minato, Shisui, roshi, Lightning main, akatsuki Monster forms, Better Narutos, basically any Uchiha, etc.