Typically, I will begin with a wireframe mockup of the rulebook in InDesign. Here I apply any large-scale changes to the structure of your rules, which may mean reorganizing sections, moving rules around, or merging together rules and sections to eliminate redundancy.
After this is completed, I do a sentence-by-sentence edit for grammar and language. I highlight any key game terms, add callout boxes and marginalia to emphasize definitions and often overlooked rules, and work with the game designer to ensure any ambiguities are resolved. I also convert all rules to active instructional language ("On your turn, do X") rather than passive descriptive ("On their turn, a player does X"). This helps readers learn and remember rules faster.
Once I am thoroughly familiar with the rules, I determine where detailed examples and diagrams are necessary, and create these using existing game assets. Typically, I design a visual components list and a full 2-page setup diagram with numbered labels corresponding to each step of the setup instructions. This will also be where I add any important reference info to the back page.
Lastly, I apply visual polish, working with your graphic designer to make the visual style of the rulebook match that of the game and its components.