Currently, to configure the WDQS UI, you have to modify the wikibase/config.js file, which is under version control: any time you want to update the website, you need to stash your own changes, do a git pull, and then unstash your changes again, hoping that there is no merge conflict. This should not be necessary.
I think there are two steps to this: we should read more than one configuration file (one default file that is under version control, and one site-specific one that isn’t and may be absent), and at least the site-specific file should be JSON, not JS. (For clarity, ideally the version-controlled configuration file should be JSON as well so that you can easily copy it to the site-specific one, and any logic that needs JS should be somewhere else. But I’m not sure about the details yet.)