What can I actually set for the ebook?
Most of the formatter's controls are about the printed page. An ebook is laid out by the reader's own device, so there are only a handful of decisions left that are genuinely yours. They're all in the ebook settings.
Where the book opens
The page a reader lands on the first time they open your ebook.
The first chapter is the right answer for most books, and it's the default. Readers who have just bought a novel want the novel; making them swipe past a title page and a copyright notice is a small tax on the first thirty seconds of your book. Choose the title page or the cover only if there's a reason — an illustrated book, or one where the front matter is part of the reading experience.
This affects the first opening only. The front matter is still in the file, and readers can go back to it whenever they like.
Contents list
The chapter list in the reading app's own menu — the one you reach from the toolbar in Apple Books or Kindle. This is not a page in the book.
- Chapters only — one entry per chapter. Right for novels.
- Chapters and sub-headings — nests each chapter's own sub-headings beneath it. Right for nonfiction with structure inside its chapters.
Every EPUB has this list either way; the setting only decides how deep it goes. The separate, visible contents page is a different thing — see Can I add a table of contents?
The ebook cover
An EPUB without a cover is technically valid and looks broken in every store, so the formatter asks for one. If you built your cover here, it's already there. If your cover came from somewhere else, you can upload a JPEG.
Hyphenation
The hyphenation switch is shared with the print book. In print it decides where words break; in the ebook it tells the reading device whether it may hyphenate at all, since only the device knows where the lines fall. Apple Books and Kobo honor it. Kindle does its own hyphenation during conversion regardless. See Should I leave hyphenation on?
What you can't set, on purpose
Font, text size, line spacing, margins, page breaks, justification. Readers control all of these, and a book that tries to override them is a book that fights the reader's accessibility settings. See Why does my EPUB look different on different devices?