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This is a question with answer. As I have figured out the easiest solution.
Here is the description of the problem -
I have successfully install a Ubuntu 14.04 droplet and hosted a domain say ‘myprimary.com’ there, the default root is /var/www/html. Further, I have installed CMS and other scripts inside it, and they are working fine. Now, I have bought another domain ‘mysecondary.com’ and want to create an all new site inside the droplet, but without moving the files of ‘myprimary.com’ (because of any downtime of this domain)