I will list and describe the standard paths to the cPanel & WHM configuration files:
/usr/local/apache/conf/httpd.conf (link to web server apache configuration)
readlink /usr/local/apache/conf/httpd.conf
/etc/apache2/conf/httpd.conf (apache web server)
/usr/local/lib/php.ini (PHP)
/opt/cpanel/ea-php56/root/etc/php.ini (PHP)
/etc/ssh/sshd_config (SSH configuration)
/etc/proftpd.conf (proftpd FTP server)
/etc/pure-ftpd.conf (pure-ftpd FTP server)
/var/cpanel/cpanel.config (cpanel configuration)
/var/cpanel/root.accts (list of root domain owners)
/etc/wwwacct.conf (account file)
/etc/cpupdate.conf (cPanel update configuration)
/etc/cpbackup.conf (backups)
/var/spool/cron/ (scheduled cron jobs)
/etc/clamav.conf (clamav antivirus)
/etc/my.cnf (mysql databases)
/var/lib/pgsql/data/postgresql.conf & pg_hba.conf (postgreSQL databases)
/etc/exim.conf (exim mail server)
/etc/dovecot.conf (dovecot mail server)
/etc/valiases/domainname (forwarding settings)
/etc/vfilters/domainname (email filters)
/etc/userdomains (list of all domains, subdomains and their users)
/etc/localdomains (list of all local domains, sub-domains for exim from which mail can be sent)
/var/cpanel/users/ (cpanel user options)
/etc/named.conf (DNS name server)
/etc/resolv.conf (network settings)
/etc/sysconfig/network (network settings)
/etc/hosts (host configuration)
/etc/nameserverips (list of name servers (NS))
See also my article:
Location of log files cPanel