There are many different kinds of non-fiction books. The most structured ones are academic books. Typically for such a book, you would need an advanced degree, you would be published through an academic press, and in connection with a specific program, which would give you their own standards. Academic books have very specific guidelines for things like footnotes and citations, but different programs use different guidebooks --Chicago and MLA are two of the most common. If you're writing for an academic audience, you'll be expected to have your own copy of the chosen guidebook, and to know it inside and out. Other specialized non-fiction niches may have their own stylistic expectations --but those depend entirely on the specific niche.
There are no such structured expectations for general interest non-fiction, although you might want to pick one of the two above stylebooks and use it, if you want your book to seem serious and well-organized. In other words, you can pattern your book after an academic book (although general-interest non-fiction's primary obligation is to be entertaining and engaging).
It's worth noting that most non-fiction, in contrast to fiction, is sold with a proposal, outline and sample chapters, rather than a complete manuscript. If your publisher has specific needs and expectations, they may ask for them at that point.