Where can I find docker daemon config file on boot2docker machine?
According to this topic: Dockerfile: Docker build can't download packages: centos->yum, de
If you want to script things, you can do these steps on one ugly line:
boot2docker ssh 'sudo sh -c "echo \"EXTRA_ARGS=\\\"--dns 1.2.3.4\\\"\" > /var/lib/boot2docker/profile && sudo /etc/init.d/docker restart"'