Keep changes in the site's own files so replacing the installed theme does not remove them.

ChangeWhere it belongs
Name, logo, footer, colors and fontsBrand and colors
Navigation, search and reading controlsConfiguration
Stylesheets, scripts and markupTemplate extensions
Available blocks and their contextExtension reference

After changing styles or templates, check the affected pages in both palettes and at a narrow width. Review those overrides when updating the theme.