Pi-Hole is the black hole for the internet. As of the most recent Pi-hole Version v2.13.2 with Web Interface Version v2.5.2, a local network should have the necessary tools, DNS and DHCP servers, to run successfully.
With that said, what if you want custom DNS settings? I tried this approach successfully, so now one IP resolves to several domain names. The following was completed as root user.
echo "addn-hosts=/etc/pihole/lan.list" | tee /etc/dnsmasq.d/02-lan.conf
Add IPs and names to a host file.
echo '192.168.1.100 test.example.com my.example.com my.server.home' | tee /etc/pihole/lan.list
Restart the DNSMasq Server. I used the web interface. However, the following command should do.
service dnsmasq force-reload
Now, the fqdn server names should all resolve to the IP address identified in the lan.list file.