|You want your Bible all in small caps?|
Now authors can pick from a huge variety of fonts and layout options at the touch of a drop down menu. What do you pick? There are plenty of sites which will give you a step by step process so I'm not going to replicate that. Instead, I'm going to talk about what some of the standard options are, what options authors should be considering and mention a few of the more common oversights.
First up, font and spacing. Most default fonts are Times New Roman, Calibri or Arial, none of which look good in a print book. The most common fonts used for novels are Garamond, Caslon, Minion, Janson Text and Palatino. However those aren't the only options. Using a common font will give a reader a sense of reassurance and professionalism, but perhaps a writer wants to use the font as part of the reading experience. I read one book which was entirely emails and the author used Calibri, which is the most common email font. It added to the authenticity and illusion. Try a number of different options and decide which looks visually best.
Standard spacing is 1.15 with the first line of each paragraph indented 0.3 inches (or 3 spaces) with no additional blank lines between paragraphs. (For the curious, paragraphs which begin with a left-flush line and have a gap between them is the standard format for web content.) Having a gap between paragraphs is a visual disruption and is usually used to signal a scene or point of view change. Using 1.5 or double spacing makes your manuscript look as if it is still in the draft phase. Using a different indentation will just look odd to an experienced reader and may end up throwing them off.
Next, page formatting. The standard for novels is full justification, with an even line down both sides of the page. It looks neat and smooth but can sometimes end up with odd internal spacing. Make sure to check the defaults for hyphenation and widow-orphan protection. Hyphenation will automatically break up longer words to avoid odd gaps, which you may or may not want. (Personally, I don't like it.) Widow-orphan protection ensures that a manuscript doesn't have a single line or two on one page, keeping paragraphs together. This can lead to odd spacing at the top or bottom of a page.
Now we can get into some of the more flexible options. Page numbers, chapter headings, headers and footers, and what to include in the front and back material.
Print books have page numbers but not necessarily on every page. I recommend checking a number of books similar to your own to decide what the best options are. Very few novels use page numbers for front or back material. Some won't use them on the first page of a chapter, or will have a different placement (bottom instead of top). Deciding where to put your page number (top, bottom, left, right, centered, mirrored) is a personal aesthetic choice.
Some authors like to use a different font for chapter headings, some use special graphics, some like a chapter to start halfway down the page, others prefer a continuous run where one chapter can end and another can begin on the same page. Some won't start a chapter on the left hand page of a book, adding a blank page to ensure it starts on the right. Each option creates a different experience for the reader. A strong break for each chapter can increase the sense of tension and enhance end-of-chapter hooks. Using a graphic or special font creates a stronger visual break.
Some authors include information in headers or footers (text which appears at the top or bottom of each page). The most common is to have the author name on one page and the book title on the other, usually at the top. It is less disruptive to a reader to have that information on the top of a page than at the bottom. Some authors say including a header or footer distracts readers, some say it provides subconsciously reinforced marketing.
Your front and back material is the non-story information which is included. Most books include a legal disclaimer and publishing information (year of publication, copyrights, etc.) at the front, as well as an internal cover page with the title and author's name and a dedication (the "To X, Y, Z"). Others include lists of the author's other books, excerpts from reviews, reading order of the books in the series, lists of characters or foreign language word definitions, quotes or other mood setters, or an overview of what has happened in previous books in the series.
The back material usually includes an "About the Author" biography, acknowledgements for those who have helped with the book, and a promotional excerpt from either the next book in the series or another popular work by the author. Sometimes several promotional excerpts or ads are included. Some authors will include research notes, particularly for historical or science fiction works. Some will include a personal note to the reader, talking about their favorite parts of the book or the writing process.
Each choice a writer makes will create a different experience for his or her readers. Decide what kind of experience you want to create: intimate, informative, invisible or something else entirely.
At the end of the day, we have a flexibility which would make Gutenberg tear his beard off in frustration. Like the official writing "rules", all the formatting rules can be broken, provided they are broken with purpose and deliberate understanding.