Well, IMO the first idea will work better. Let me explain my point of view : if the secondary villain gets manipulated by the main one, the story will end up with two villains that are roughly the same type, one being the "clone" of the other.
As for the first idea, at the beginning the situation should be as I said previously, two versions of the same villain, and then, if the secondary villain gets into "true darkness" as you say, it will cause, first, the character to become deeper, and then, the story to be more enticing.
And if your story is long enough, you can make that character start out good, then he is manipulated, then he realizes he was manipulated and becomes truly evil. But well, that's maybe too much evolution for one single character.
That was my opinion. But well, it's your story, and you do what you want with it.
As for the first idea, at the beginning the situation should be as I said previously, two versions of the same villain, and then, if the secondary villain gets into "true darkness" as you say, it will cause, first, the character to become deeper, and then, the story to be more enticing.
And if your story is long enough, you can make that character start out good, then he is manipulated, then he realizes he was manipulated and becomes truly evil. But well, that's maybe too much evolution for one single character.
That was my opinion. But well, it's your story, and you do what you want with it.