When you add a domain name to your account, you can choose to either set it up as a standalone website, or as an alias to another website. If you add it as a standalone site, the website will get its own, dedicated directory.
If the website you’re looking to use is in a different directory and there is a domain on your account that’s currently linked to that directory, then you can remove your domain and add it again, but this time choose to make the domain an alias of the existing domain.
If that’s not possible for some reason, then you can always just move the website to the directory of the domain you want to host the website on: