An easy way to pull all of your phones system app, jars and res files is to use Xeudoxus's script file found here:

[app/script] xUltimate v1.2.4 **UPDATED 02/17/10**

The file is designed to do more, but you can do the first couple of steps and have your pc pull all the files you might want to theme. You just need to have adb working. The upside is it will snag all the files, and store them safely on your pc. If you work on files in a seperate location, this could also be helpful to undo something that goes badly.

I am sure there is likley an easier way to do this, but this does work, and it sets the files up in a nice directory structure on your pc.