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).
Because Yii intends to be integrated nicely with third-party libraries, it does not define any global functions. Everything in Yii needs to be addressed with full class name or object scopes. For example, to access the current user, we need to use Yii::app()->user; to access application parameters, we need Yii::app()->params['name']; and so on. While editors like textmate can help alleviate the problem of these lengthy typings, it is worthwhile to define global shortcut functions to some commonly used method calls. They will make the application code look cleaner.
Sometimes we get lost trying to search by a HAS_MANY relation using CActiveRecord or CActiveDataProvider in Yii 1.1. This article is a series of drills that try to describe the practical techniques of searching by a HAS_MANY relation.
A simple and effective way to keep track what your users are doing within your application is to log their activities related to database modifications. You can log whenever a record was inserted, changed or deleted, and also when and by which user this was done. For a CActiveRecord Model you could use a behavior for this purpose. This way you will be able to add log functionality to ActiveRecords very easily.