Please explain WP file structure – new user

I now know how to copy a WP sight to a new domain. That is not the question. I just want to understand how WP files things.

Note: Before I did anything I had zipped and downloaded the site folder which I thought would contain everything I need. Apparently I was wrong.

1. While spending a day to figure out the site transfer, I made my original inaccessible by changing the settings/URLs to the new location per instructions of an online poster (GRRR#@!!). I got a redirection and error. Not to worry I thought, I had downloaded the original site folder two days earlier.

2. So I upload the backup site and it does the same thing. It redirects to a folder that did not exist when I downloaded it two days earlier.

So as far as I can see, WP must file the database somewhere else. Can someone kindly tell me what’s going on here?

Thanks for your help!