This maybe a dumb question, but here goes. I am going to be doing the manual upgrade to Cyanogenmod 9 and with the upgrade rolling out again, possibly a revised one? to me AGAIN? will it try to overwrite the Cyanogenmod 9? If so, is there a way to prevent this? or should I wait until after the revised? upgrade does it's thing so I don't have to do the manual upgrade twice? :-\
There are no dumb questions, only dumb answers. Hopefully my answer doesn't fall into the latter category.
When you flash a ROM like CM9, you are really not upgrading anything. You are simply flashing an entirely different operating system. This is very different than taking the manual upgrade file that contains the data of the official OTA update, and installing it.
To answer your main question, once you flash CM9, or another other AOSP based ROM, you will not be notified that there is a system update available for your phone via the network. Even if you somehow did and were able to download it, the install would fail in dramatic fashion. It would have no idea how to update the system sitting on your phone at the time. Still, this wouldn't happen. You'd never be prompted to update.
If you were to flash a modified Samsung Touchwiz ICS ROM based on the most recent official release version, you also would not receive update notifications, because the system would think you already updated as it would see you're on the current software version. If another update came out later, you would be notified of an update in that case, but again, the update would fail, because the system on your phone was not 100% stock.
In the end, once you start flashing software to your phone, you'll never worry about OTA updates again, as they basically become irrelevant. For an example, I had the FF18 official ICS ROM on my phone for about a month before the update was officially released. The OTA meant nothing to me, because I was essentially running the end result for weeks already.