It doesn't help that the in-game explanations are deliberately vague and shrouded in mysticism - and even, at times contradictory of one another, as different factions believe different things about the gods.
For example, something not mentioned on the wiki, but seemed crystal clear to me after completing the game, was the fact that Altana and Promathea were lovers. They were beloved to one another, and while in opposition due to being beings of light and darkness, respectively, loved each other dearly. Promathia, however, wished for his own death, and eventually succeeded. Altana's sorrow at this is what caused her to weep the tears the became the five player races.
Is this the truth the developers intended? I'm not sure; it's what I believed after viewing the cutscenes from the various expansions. Different folks may have different interpretations. And, like almost EVERY aspect of FFXI, the developers aren't telling us anything about what's going on. XD
Here's something significant that I took away from Rhapsodies of Vana'diel:
The metaphorical "wind" generated by the conflict between the two gods is what was keeping the Cloud of Darkness at bay, and the only thing protecting Vana'diel from being consumed by the Cloud, as so many other worlds are. When Promathia died, this wind died down as well - but the conflict between Promathia's children (the beastmen) and Altana's (the player races) was enough to hold the Cloud at bay.
At least, it was until recent times when the races started to find an unsteady peace. Then, the Cloud began to encroach once more, eventually leading to the Bad Future the expansion's heroine had come back in time to prevent. Eventually, the player is able to shoo the Cloud away once again by ascending to "light" godhood and doing battle with his or her future self, who happened to have ascended to "dark" godhood.