I almost forgot - For the last few versions (I dont know since when off the top of my head), timthumb has allowed for a config file, named timthumb-config.php, and stored in the same directory as your timthumb instance, to override default timthumb settings.
By using this, you can maintain any settings you'd like, without having to worry about updates overwriting them.
Unfortunately, I can't really find any documentation or examples right now - but here are 2 things to get you started:
http://timthumb.googlecode.com/svn/trunk/timthumb.php (start reading at "--- TimThumb CONFIGURATION ---"
Hope that helps!