The article Fixing extensions without modifying their code reminded me of another patching technique that I used. My conviction and a hard look on the web had led me to an article Redefine PHP class methods or class giving me a head start to do what I wanted: patching third party code without touching the original to allow easy upgrades.
Using CActiveRecord->updateAll() and CActiveRecord->deleteAll() with scopes and criteria requires some tricks that are explained in this article. While findAll() , find() and some other methods use scopes automatically, updateAll() and deleteAll() do not.
I found a standard Yii app's protected folder structure nearly perfect. With a few simple moves and a little bit change to the code, I managed to bring it to the level, which I found as fully perfect. I want to share my point of view, in case someone would like to use this structure as well.