You always create a website as if there are going to be others. It means the first level of content nodes in root are the different websites hosted (Except if you are Scaffolding)

Due to the positioning of the Website node in the tree hierarchy, it means any request for a local webpage will always have a Website node as a direct ancestor, this allows for quick retrieval of setting information.

As for what should be Settings, here's a few ideas

While it is very true for development reasons there will be seperate Umbraco instances for testing and staging code, as well as user sign off for example, this doesn't mean that the same holds true for Content. A common pitfall is creating a seperate Umbraco instance for Content Editors to test and evaluate content and then 'solutions' are created to move this content between environments.

All this unnecessary work doesn't need to happen, instead just create a staging website inside the same Umbraco instance as live. Restrict access to this domain as required and volia, Content Editors can create and stage content as they please and when they need to 'push' it live they can use out-of-the-box copy functionality that has always existed within Umbraco to copy nodes, properties or relevant data between staging and live.