Yeah, I have a similar question... the UI Save button updates /etc/dnsmasq.d/01-pihole.conf with:
server=1.1.1.1
server=9.9.9.9
But, it's not obvious how to do this from the CLI when manually updating /etc/pihole/setupVars.conf.
pihole restartdns does not update dnsmasq.
Maybe updating upstream DNS servers from the CLI should be a feature request?