Remnantan Pantheon is not a centralized religion, but it varies between regions. Two Brothers could be the reformed version of it, possibly having heresies.
Hm... How non-centralized is it? Forgive me if I sound a little too overstepping, I understand you have little to work with, but differing religions are a major part of CK2, so I feel there should be quite a bit of variety. A few ideas I could have would be... Hm...
The Two Brothers, of course most likely as a reformable faith related to a theoretical story event chain (though of course spawnable in other ways too). Mayhaps with heresies worshipping, instead of both of them duotheistically, only one of the brothers, with the other being a satan-figure (The brother of Creation's cult being a traditional, almost christian-esque faith, while the brother of Destruction's is more akin to Gnosticism with the brother of Creation being a childish Demiurge.)
A faith based around the wizard and the maidens, who are apparently a major religion if vol 3 is to be believed (They mention it would cause religious chaos among other things, so its clearly a proper religion that people know about instead of
just a fairytale.)
Perhaps a faith that directly worships Aura as some kind of holy force in itself, maybe with a deep spiritual tradition of animism akin to shintoism and set in Mistralian territories.
Menagerie could have a more faith-esque ideological movement based around freedom rather than a proper religion, with the White Fang as a heresy.
A personality cult based around the Last King of Vale, a la Alexander the Great.
Maybe as the Atlas arc coming up shows more Atlesian culture we may get more hints for theoretical religions. As it stands maybe it could have a "Cult of Reason" vibe to it.
Vacuo is a bit of a crapshot considering we know so little about it... Might have to just make something up entirely and not get too attached if canon throws it out the window...
I understand that you have a lot on your plate with this, but since you have to make up a lot of stuff anyways lore-wise, might as well make up the religions since they don't seem to have much impact on the story. Minus the two stated to be "True" by the big good.
Edit: Again, if I'm overstepping my boundaries, feel free to ignore me if you feel it necessary.
Edit 2: I just remembered that... I think Sun or Ilia said something about Vacuo "accepting you so long as you could survive. Maybe that could be grouped in with the Menagerie and Atlas faiths as "state sponsered atheism" type faiths. And there was a common joke in the early days of rwby (that may be more or less still around. I havent really been into the fandoms injokes lately) about Monty being the in-universe God. Maybe that could be some kind of joke heresy for the Two Brothers. Or even the default faith of Vale? (Maybe just Patch so its not too prevelant but still has a foothold.) But I can understand why you wouldnt want a joke-based faith to be the default, I'm sure.