That will be because the domain is controlled by your other user. To change which user controls a domain, go to Domains -> Manage Domains in the panel, click the small Edit link for the relevant domain (in the Web Hosting column). You can then select the FTP user / CGI-runs-as user: using the drop-down box.
Not really. As far as I know, your initial user is no more important than any other user you create. Just be sure that this user does not have any important data etc. in their home directory before deletion.
Edit: Note, changing the user that controls a domain will create an empty web-directory for that domain in the users home directory, but it will not automatically copy the contents from the previous web directory in the other users home directory. You will need to do this manually (or upload the files again).
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