Hey there. You may want to look into BBEdit 6.5 - when you try saving a file that is not owned by yourself, BBEdit 6.5 will bring up a dialog asking for a valid password. It's transparent authentication.
Ignoring the above, no, you don't have to login as root to mess with the config file. What you want is something called 'sudo', which allows you to run commands as a different user.
You can find out more about 'sudo' in the Terminal: Part 1 article, also at O'Reilly. Check it out here: http://www.oreillynet.com/pub/a/mac/2001/12/14/terminal_one.html