I think whoever knows, knows - this howto is for the ones who mess up their systems frequently.
If you have a live install + changes, an easy way to backup your system would be:
Let's assume your changes partition is /dev/sda2. It's mounted in /mnt/sda2, and when you cd into /mnt/sda2, you see the changes folder.
tar -cvvf changes.tar.gz changes/
this will archive your changes, do that before every major apt-get update && apt-get upgrade, or before you install some huge application that could possibly require hours in configuration and hours of messing up after you mess up...
I do that now every so often, and this way my backup keeps being in the small sizes of 100-200~ megs. Pretty sweet! Close to rsync, but easier.
Then, once you mess up, you just do a
tar -xzvf changes.tar.gz
in the same place, and voila, your system is restored....