Does the domain show via the ‘manage domains’ page in the panel? Does it show as ‘fully hosted’ in the web hosting column? What user is listed right under the words “fully hosted” for the domain? Are you logging in on ftp with that user? When you log in with that user you will be in that users HOME directory, If you have added all of the above that directory will contain a directory called, you should change to that directory and place your files there.

In each case above your answer should not be “no”, the questions are ordered so that we can figure out what went wrong.