Just as the Demon Realm was divided among the Six Great Demon Lords, with each Demon Lord possessing her own territory and all demonkind within it falling under her jurisdiction, the God Race had its own hierarchical system despite having no concept of divided territories.
The Three Great Goddesses naturally governed all of the God Race, but they did not govern them as a single unified body. Each had her own sphere of authority.
Just as humanity was guided by one of the Three Great Goddesses, every high-ranking god and low-ranking god within the God Race had someone they belonged to.
For example, Lilith the Evil God, the strongest evil god, was a high-ranking god under Goddess of Life Anima's jurisdiction. That was why Anima had deliberately kept the Beastmen Race guarding the temple that sealed Lilith. Whenever something went wrong with Lilith's seal, Anima was always the first to react and take action. That relationship was the reason.
Meanwhile, Goddess of Justice, who stood opposed to Lilith, belonged under Goddess of Fate Lidas's jurisdiction. The division of responsibilities was clear.
Of course, because the Three Great Goddesses were close-knit, these affiliations merely made it easier to govern the God Race. They were not meant for them to form separate cliques or little groups. Thus, while the goddesses normally only obeyed the Three Great Goddess they belonged to, they would likewise listen when either of the other two goddesses gave them orders.
At the end of the day, the God Race's hierarchy had long been clearly established. At the top stood the Three Great Goddesses, followed by high-ranking gods, then low-ranking gods. Low-ranking gods had to obey high-ranking gods, and high-ranking gods had to obey the Three Great Goddesses. That was an eternal hierarchy.
Therefore, a goddess's affiliation truly existed