Yes, you need to put a proper plist into /private/var/root/Library/Preferences.
You can do it one of two ways:
a) Terminal.app
b) a PKG file that you create in Composer. I typically enable the root user on a test machine, log in as root, configure the Dock (and also Safari - homepage) the way I want, then log out/log back in and manually create a PKG in Composer that has these two files. I then add this PKG to my AutoCasperNBI workflow. And hopefully I don't forget to disable the root user login (usually do this on a machine that's about to be re-imaged ;-)
This works, but if @bentoms][/url][/url wants to come up with an easier way to do this (since I build AutoCasperNBI images for literally a dozen or more clients, I'm often editing the plists and creating PKG files for each client), that would be awesome ;-)
--Robert