Classic Sci Fi Trope; the evil side always has red eyes or glow, the good side is usually represented by blue or whitish energy.
That's why the whole thing got awkward at the end. Trek has always tried to avoid too much religious symbolism, but DS9 jumped right into it.
I always found episodes with the Prophets fascinating, but the last few episodes were too much.
The Pah Wraiths started off as simply enemies of the Prophets, but then morphed into super evil beings that wanted to set the Galaxy on fire or something.
The showdown between the two "chosen ones" was too comic book like for me, I'd rather they did it another way.