Hello,
I am using the same hosting and it’s normal that addon site appears on 2 locations. This is my example (this is Hot Architecture template).
Main site is http://www.arhinet.net/
Addon domain is http://www.arhitektura.rs/
However, you can see the addon doman also here http://www.arhinet.net/arhitektura.rs/
This is how cPanel works and we can’t change this. This is not a template issue.
I hope I understand your problem well. If not, please let me know.
Thanks