Mannfred pretty distinctly would have made his library after Konrad's reign, he certainly didn't return to Sylvania until his rivals were well and dead.
I think plenty of people would consider a chamber below the castle that can only be accessed from the castle to be part of the castle.
A different page of the Vampire Counts book makes it clear that he did indeed return only after Konrad died, whereas the one I looked at before seemed to say it was before he died. Seems I was wrong on that count. I've still got reason to believe it's two different libraries.
Firstly, we've got this from the last main turn update.
[ ] The many legends about the amount of books contained within and under Castle Drakenhof still haunt you. Organize an expedition to mine the ruins for books. (NEW)
If Mannfred simply moved his books into the subterranean library or vice-versa, I think it's pretty unlikely there'd be two separate sets of legends.
Besides that line, the information in Night's Dark Masters does most to make it seem they were two different libraries.
The section on the Black Library didn't mention Mannfred at all, which you think it would've if he'd dumped his books there. It's not simply a matter of the authors having forgotten about his library, because it's mentioned in comparison to von Sangster's library.
Perhaps the biggest argument for them being two separate libraries is Immoliah Fey. There's no source for him anywhere but Night's Dark Masters. He's an original invention of the book, and he only shows up in the Black Library section. They very easily could've said Mannfred made the library but decided to create Immoliah instead, and making the libraries separate is the only reason I can think of.
Then there's the fact that Immoliah was the one who made the chamber huge. If he did that, it's because he had enough books that he needed the space. I don't think Mannfred with his own treasure trove of lore taken from all over Nehekhara would've fit with all the existing books.
Though I have to say, I really wouldn't mind if Mannfred managed to fit his books into Immoliah's library. It means that both gigantic hoards of books would've survived the bombardment in their entirety, which means more books for us. I just don't think they are in fact the same library.