Apache httpd.conf Issue

Hello, I have CentOS release 6.8 (Final) with WHM Latest. First now when i goto WHM my Easy Apache is changed with Easy Apache4. My issue is, i want make one entry for IP in my httpd.conf and want that entry to stay. before i do this in this way, i goto SSH and type this command httpd -V This gives me location of httpd.conf file, so i got there cd /etc/apache2 cd conf nano httpd.conf and make changes in httpd.conf and save & exit and restart Apache and it works. to Make changes permanent i goto /usr/local/apache/conf/httpd.conf Make my changes under NameVirtualHost and these changes stay, even after apache rebuild or server update. Now my problem is that after making changes in /etc/apache2/conf/httpd.conf i can see same changes in /usr/local/apache/conf/httpd.conf and these are automatically done. how to make changes stay even after apache rebuild and how to find that file. Thanks