I think you've got it right now... ;)
I am not an English grammarian, but my "grammar ear" is well trained by vast amounts of reading.
The difference here has to do with the word "does," so that as you have said, "how it manifests" would be correct, but "how does it manifest" is correct as you now have it, as would be "how it does manifest."
Thanks :)
You're welcome, and thanks again for a cool new word to roll off my tongue! ;)