If I understand correctly, you are asking which directory you should upload your files to. You should upload your pages to example.com directory as this is your domain directory.
Here is how DH manages directories.
- Each user has its user directory /home/username
- Each domain has its domain directory in its user directory. /home/username/domain.com
- If user manages multiple domains, it would be /home/username/domain1.com and /home/username/domain2.com
Web pages should be uploaded to the correct domain directory.
Hope the above helps a bit