Pillars of Eternity II: Deadfire features a variety of factions and the Watcher's choice of alliances and antagonists will have a marked effect on the result of the Hunt for Eothas.
Your standing with the factions is determined by your reputation which is tracked on two axes: Positive and Negative. These determine how you are treated. Every point of positive reputation gives you a -5% discount at any faction store, and each rank can give you unique options in dialogue with faction affiliates. Most quests will also present you with a variety of outcomes which generate different reputation effects and benefits.