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).
I have been trying to find information on how to sync the sessions between Yii and KCFinder so that the two applications can "communicate" with each other. I managed to find some bits and pieces on the correct approach to use, but not a definite guide or concrete code.
A big problem I've hit with the Yii-Bootstrap extension is that all AJAX requests are initializing Bootstrap because of preload. This is a huge waste of resources, especially when using AJAX-based file uploaders that split the file into chunks. Large file uploads using that method could be initializing bootstrap hundreds of times.