I've a 3 router network wherein 1st router is at Ground floor - modem/router provided by ISP at LAN IP 192.168.1.1 (WIFI disabled) and DHCP pool size set to 2, 2nd router is too at Ground floor (WIFI enabled) with WAN at 192.168.1.2, LAN IP 192.168.50.1 with DHCP enabled and DHCP pool size set to 200, lastly 3rd router is top floor (WIFI enabled) with WAN at 192.168.50.2, LAN IP 192.168.51.1 with DHCP enabled and and DHCP pool size set to 200.Changing DNS settings would disrupt your internet if not properly configured. Can you describe more of what IP and DNS settings you are using on both your Pi-hole and connected devices?
A couple of assumptions that may not be correct. You have some device running pihole on your network and you have a different device running as your router. You are attempting to set the DNS in the router wan settings.
Most routers are pretty dumb they expect the DNS server to be on the internet. They will not forward DNS traffic to a server on your lan.
What you would need to do is either manually set the dns server in the nic setting on the end device or set the DNS in the DHCP configuration on the router to point to the pihole server. Not all router support setting the DNS in the DHCP settings.
Although even more complex you should be able to disable the dhcp server in the router and use the Pihole server to do the dhcp function being careful that it sends the router lan ip as the gateway.