How do I set my DNS when resolv.conf is being overwritten?

I believe if you want to override the DNS nameserver you merely add a line similar to this in your base file under resolv.conf.d.

Example

$ sudo vim /etc/resolvconf/resolv.conf.d/base

Then put your nameserver list in like so:

nameserver 8.8.8.8
nameserver 8.8.4.4

Finally update resolvconf:

$ sudo resolvconf -u

If you take a look at the man page for resolvconf it describes the various files under /etc/resolvconf/resolv.conf.d/.

   /etc/resolvconf/resolv.conf.d/base
          File  containing  basic  resolver  information.  The lines in this 
          file are included in the resolver configuration file even when no
          interfaces are configured.

   /etc/resolvconf/resolv.conf.d/head
          File to be prepended to the dynamically generated resolver 
          configuration file.  Normally this is just a comment line.

   /etc/resolvconf/resolv.conf.d/tail
          File to be appended to the dynamically generated resolver 
          configuration file.  To append nothing, make this  an  empty  
          file.   This file is a good place to put a resolver options line 
          if one is needed, e.g.,

              options inet6

Even though there's a warning at the top of the head file:

$ cat /etc/resolvconf/resolv.conf.d/head
# Dynamic resolv.conf(5) file for glibc resolver(3) generated by resolvconf(8)
#     DO NOT EDIT THIS FILE BY HAND -- YOUR CHANGES WILL BE OVERWRITTEN

this warning is is there so that when these files are constructed, the warning will ultimately work its way into the resulting resolv.conf file that these files will be used to make. So you could just as easily have added the nameserver lines that are described above for the base file, to the head file too.

References

• Persist dns nameserver for ubuntu 14.04
• How do I add a DNS server via resolv.conf?

I am also interested in this question and I tried the solution proposed @sim.

To test it, I put

nameserver 8.8.8.8

in /etc/resolvconf/resolv.conf.d/base and

nameserver 8.8.4.4

in /etc/resolvconf/resolv.conf.d/head

Then I restarted the network with

sudo service network-manager restart

The result is that /etc/resolv.conf looks like

# Dynamic resolv.conf(5) file for glibc resolver(3) generated by resolvconf(8)
#     DO NOT EDIT THIS FILE BY HAND -- YOUR CHANGES WILL BE OVERWRITTEN
nameserver 8.8.4.4
nameserver 127.0.1.1

and nm-tool states that the dnsserver are

DNS:             208.67.222.222
DNS:             208.67.220.220

which are the ones provided by my router. On the other hand digging an address tells that

;; Query time: 28 msec
;; SERVER: 8.8.4.4#53(8.8.4.4)

If I am right, I conclude from all this that

1. only the "head" part is read by resolvonf: the "base" part is somehow controlled by dnsmasq
2. the dnsserver is actually forced to 8.8.4.4 regardless of the server provided by dhcp, BUT you loose the caching provided by dnsmasq, since the request is always sent to 8.8.4.4
3. dnsmasq is still using ONLY the dnsserver provided by dhcp.

All in all, it works but I don't think it is the intended result asked for. A more close solution I think is the following. Edit

sudo vim /etc/dhcp/dhclient.conf

then add

supersede domain-name-servers 8.8.8.8;

The result is the following: resolv.conf contains only 127.0.0.1, which means that dnsmasq cache is invoked and nm-tool says

DNS:             8.8.8.8

which means that if the name searched for is not in the cache, then it is asked for at 8.8.8.8 and not at the server provided by dhcp.

Another (perhaps better) option is to use "prepend" instead of "supersede": in this way, if the name is not resolved by 8.8.8.8, then the request falls back on the other server. In fact, nm-tool says

DNS:             8.8.8.8    
DNS:             208.67.222.222
DNS:             208.67.220.220

I found out that you can change the nameservers that dnsmasq uses by adding the following lines to /etc/dnsmasq.conf:

server=8.8.8.8
server=8.8.4.4

I didn't have a /etc/dnsmasq.conf file though, since it's installed by the dnsmasq package, but Ubuntu only comes with dnsmasq-base. I ran sudo apt-get install dnsmasq, then edited /etc/dnsmasq.conf, then sudo service dnsmasq restart and sudo service network-manager restart.

I ran sudo tail -n 200 /var/log/syslog to check my syslog and verify that dnsmasq was using the nameservers I specified:

Oct 21 23:00:54 mylaptop dnsmasq[8611]: using nameserver 8.8.8.8#53
Oct 21 23:00:54 mylaptop dnsmasq[8611]: using nameserver 8.8.4.4#53