Say you want to change something which persists reboots, like /etc/initrc (http://unix.stackexchange.com/questions/17470/why-does-ctrlarrow-make-my-terminal-switch-to-a-strange-mode) then do this:

1) Mount the filesystem writable with: mount -uw /
2) Edit the desired file(s) in /etc/
3) Edit the desired file(s) in /conf/base/etc/
4) Remount the filesystem read only with: mount -ur /

Obviously this will reset itself after upgrading the filesystem such as in case of a major FreeNAS upgrade.