When you login to ftp you are placed in your home directory. /home/USERNAME/
You should see a directory that was created automatically when you added hosting for yourdomain. If you accepted the panels default that directory will be named the same as your DOMAINNAME.COM
Change into that directory /home/USERNAME/DOMAINNAME.COM/ this is where you will want to upload.
If the DOMAINNAME.COM directly doesn't exist, then you might be logged into the wrong ftp user for this domain.