You dont need to change the settings per qube at all.
You haven't said *where* the pi-hole qube is located in your qubes
network, or what the nature of the breakage is.
I assume from what you say it is attached to sys-firewall.
You can do this by editing the PR-QBS chain in nat table in
sys-firewall.
By default, this forwards all DNS traffic to 10.139.1.1 and 10.139.1.2
using dnat. Flush that chain and replace it with dnat rules to the IP
address of your Pi-hole qube.
You could do this in /rw/config/qubes-firewall-user-script or by script
in /rw/config/qubes-firewall.d