Having determined the core activity and design throughline, I outline, and thus structure, the book. I ask myself first of all if either of the fundamental elements call for a nonstandard structure. If not, I start with a chapter order arising from the idea of a core activity. A roleplaying game is about the characters and what they do. Ergo, the book should start with character generation. Often this entails the provision of enough context about the setting to make decisions about the characters players are designing. So I likely kick off with a quick overview of the world, universe or what have you. The rest of the first section of the book follows the step-by-step of character generation. Into this process I try to build mirrors of the design throughline: the listed decisions, and the order in which you make them, arises from the core subject matter and emotional experience of the game. HeroQuest wants you think of your characters as part of a narrative and so (among alternate choices) asks you to start with a 100-word prose description of your character. DramaSystem focuses on drama and so asks you to first establish your role in relationship to other characters and the two opposing poles that will drive your actions. GUMSHOE privileges investigation over other activities and so presents the investigative abilities before the general ones.
Subsets of character generation then appear, from most to least important, from universal to those germane to only certain character types. Almost every designer does this, whether they articulate it this way or in some other manner they find intuitive.
After this come the core rules, which enable you to understand the stuff you've just written on your character sheet. For complex resolution systems an introductory precis may appear up top, with more detail later on, so that players understand enough to make good decisions.
After this I usually cover the setting material, because it's more fun to read, and perhaps more specific to the game, than explanatory material like GM support and play style advice. The further into a book I get, the less I expect players, rather than the GM, to grapple with its contents.
Then, if the game uses them, comes the sample adventure. Given the choice I try for as complete an example as possible. I look on the sample scenario as an extended play style example and setter of expectations. My feeling is that a truncated or perfunctory scenario that merely tries to teach you the rules is a missed opportunity at best and actively misleading at worst.
Last come the appendices, reference sheets, and other bits of useful support material that aren't part of the body of the book per se.
Whether you order things like I do or not, the careful thought you pour into this question may not matter. A certain percentage of people jump around in roleplaying games to find the bits that most interest them, and then fill in the gaps. But even as they do so, they likely notice the structure and, subliminally if nothing else, learn what you're telling them from your placement order.