I assume you are familiar with accessControl standard filter. It allows you to separate privileges to run some action from action code itself. There is however one problem with most common usage - you cannot use bizRules, at least based on some parameters passed to 'checkAccess' just because it is hard to pass them in accessRules() result.
I have seen a couple of articles about how to integrate external libraries to debug our PHP code (i.e. firePHP) but after you read this article you will realize that there is no need for such libraries when using Yii.
Yii's by-default directory organization works well enough, but there are several steps one can take that improve the security and serviceability of the system, especially in the context of multiple Yii projects on the same machine (including multiple versions of the same project).