They key is that you need access to manage domains, and perhaps manage users in the panel.
When you add the domain as "fully hosted" on the "manage domains" page of the panel it will create in the users home directory on the server a directory with the same name as the domain name. That is where you will put files you want apache to find. assuming your domain is example.com and the user you have configured is jondoe then
the full path to example.com on disk would be /home/jondoe/example.com
but remember when you log into ftp you are already going to land in /home/jondoe/ by default and there you should see example.com as added by the system when you added the domain in the panel on manage domains.
the system will also add a quickstart.html file to example.com - it's the file thats served until you add your own index.php or whatever to that directory. You can delete quickstart.html as soon as you are ready.