Can I change a fighter's perks?

Not the way a loadout game works. You pick a fighter whose five perks match how you play.

What is the best perk in UFC 6?

The one whose Flow Boost you will actually repeat. A 'top' perk you never trigger is dead weight.

The perk catalog on this site lists Base Effect, Flow Boost, and Flow State for all 30.

You do not equip a loadout in ranked. The perks are already on the fighter. 'Building' means playing the bonuses you actually have.

How to read UFC 6 perks for a striker, a wrestler, and a counter fighter — the fighter already has the kit.