You can work with the files from the panel here by going to Domains -> Manage Domains and click WebFTP. You can manually move each file to the parent directory, or just try to delete the WEBSITE directory. Whatever you tweaked to make WEBSITE the root directory, get rid of the WEBSITE part of the field.
Secondly, you need to have a file called index.html in order for your site to load automatically when someone visits your URL.
p.s. Deleting that root (WEBSITE) directory isn't a very high priority, as your site will run with it still there if you successfully re-upload to the proper directory. that current root directory will just be a dead folder you can delete later.