I have an HTC and use ClockworkMod to load the updates. There is no having to redo anything. It keeps all the settings.
Why do you choose to do it via ClockworkMod, rather than the built -in CyanogenMod updater? How often do you do the updates? Every time a new nightly build is released?
There wasn't much thinking about it I used clockworkmod to root it and it's resident in the phone. So, it's just a matter of booting in to that.I've been following their build schedule when I remember and load the latest when available. I've only had one that was a little flakey.