magento 2 setup on ubuntu 14 with Nagios on sub domain for monitoring and Zpanel - linux

I am new to Linux command line and setting up Magento 2.1 on my VPS. I am thinking to setup Nagios on subdomain so i don't want any interruption on my actual domain ecommerce application.
I have few doubts which causing lot of trouble to me.
By default Zpanel comes up with lower config for Php and Mysql and to make them work with Magento 2 i have to manually upgrade them . I did that but Magento worked, whole Zpanel navigation stopped working. So i re-installed whole ubuntu Os again and ready with my box. I would also like to have Varnish Cache along with some web based console so that i can easily manage my virtual hosts and for some other stuff.
What will be the best approach to setup everything one by one on one domain/sub-domain? I have found so many articles to install magento 2 on ubuntu using command line but they dont use any webpanel. I am open to switch it to any other OS as well.
If there is sequence to setup these all, please guide.
Final Requirement:
Magento 2 with any Linux OS
Nagios server for monitoring
Web panel like CWP or Zpanel etc.
This question will be complete solution and will helpful many other users as well. All answers are highly appreciated. Thank you all in advance.
Regards
H

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