Yes, you would have to use either FTP or SSH (or Telnet, yuck). SSH can be used as long as you have the latest update version, and use a good SSH client. Safer than regular ftp.
You will find the skeleton files in /home/httpd/vhosts/.skel/
but since you only want the single domain, you don't have to worry about those skels.
You can upload a new skel tar/gz file through the CP.
The Plesk CP has many limitations..., but we must be suckers for abuse since we keep using it and paying them for the privilege...lol
Back to your problem, so you already replaced the original files with your own. Seems silly, but did you make *sure* you had the same exact filenames? Including case sensitive lettering?
And did you restart Apache after you did it?
And make sure your browser cache has been cleared.