The issue you're having is because ubuntu makes the temporary guest account (the account that you use when you boot the CD) based off of a folder named /etc/skel. In fact, whenever ubuntu needs to make a new user account, it will copy the contents of /etc/skel to the folder of the new user account.
So whatever you want to be copied to the home folder of the installed/live user (such as the theme configuration files/folders, your "Images" directory, etc...), you need to copy it to /etc/skel. Just treat it as a home directory and then you should be fine (as long as you don't copy over your web browser history and such ).
I figured out a trick a while ago that helps with copying the correct files (as it can be hard to figure out which configuration files to copy over), I don't know if it could help you too. It's to run any configuration programs you use (such as ubuntu-tweak, gnome-control-center, or ccsm) like this (replacing insert_program_name_here with the name of the program, of course), under a terminal window:
It will then run that program, making it think that your home folder is actually /etc/skel, so it will modify that instead (and then will modify the correct configuration files).
Anyways, hope this helps!! Let me know if I'm not clear or anything