Use User Access Manager with Media Files Folder plugin

I really like what this plugin offers so far, but I ran into a small issue that hopefully someone can tell me how to fix.

I use the Media Files Folder plugin to organize my photos, as I have A LOT of them. This plugin allows me to lock files uploaded normally through the media uploader, but files uploaded and organized can’t be locked. IS there a way around this?

The files are still uploaded with the media uploaded, but the paths change, so instead of it being example.com/wp-content/uploads/xxx.jpg it now becomes example.com/wp-content/uploads/examplefolder/xxx.jpg.

I enjoy this plugin so far, and can’t wait to hear some suggestions. Thanks in advance.