Just thought I would summerize all this (if its not completely clear yet)
If you are rooting to simply have some control over stock apps (killing all the ATT crap, like the address book back up that just wont stop!) then the best way is to root and freeze those apps. When you are ready to do an update just unfreeze those apps first and then ask for the update. When update is complete then re-freeze the apps. So far all the OTA updates have looked for specific changes to system apps for a clue that you are rooted. If it finds all the system apps intact, you will receive the update and most likely keep root.