Proper Method to Manage DNS

I like to occasionally change my DNS. While using Ubuntu 12.04 I had no issue manging DNS preferences through the Network Manager GUI under the IPv4 settings. Back in May I updated my OS to Ubuntu-Mate 16.04. I went along managing my DNS like I use to though the Network Manger GUI assuming changes were being made until one day when I visited ipleak.net and noticed any changes I made through Network Manger did not take.

NetworkManger.conf does not indicate any nameservers. Doing command “$ nmcli -t -f IP4.DNS device show enp2s0” lists the nameservers configured via Network Manger GUI. However, ipleak.net indicates I am using the nameservers listed in my resolv.conf file. Is the resolv.conf file the only way to manage my DNS? What is the proper way to identify DNS of choice?

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Proper Method to Manage DNS