You asked a simple question - how do I overwrite /etc/resolv.conf from
Qubes default?
The simple answer is:
Put a line in /rw/.config/rc.local like this:
echo "nameserver 9.9.9.9 " > /etc/resolv.conf
That is the simple answer to the question you asked.
The difficult t you have is that your problem is not encompassed by that
simple question.
That is why I told you you would have to deal with the warning message
that you received.
etc/resolvconf/update.d/libc: Warning: /etc/resolv.conf is not a symbolic link to /run/resolvconf/resolv.conf
If you had spent 5 minutes in the past week of travail searching for
that issue, then you would have found a solution to your actual
problem.
Try these lines in /rw/config/rc.local:
rm /etc/resolv.conf
ln -s /run/resolvconf/resolv.conf /etc/resolv.conf