In the long run, it is good to structure your settings. Because when your Chrome extension grows with new features, you can easily find that setting for that feature.
For example, if you create a Night Mode function, you can add the color for "text", "background", "button" and "hyperlink" inside.
But avoid using this way:
chrome.storage.local.set({setting1: "xxx"});
chrome.storage.local.set({setting2: "xxx"});
chrome.storage.local.set({setting3: "xxx"});
Another tip:
Try using "sync" if you want your users to get the same settings for all his other Chrome profiles. It works the same as "local".
Thanks,
Stefan vd