Sub-folder Access: Individual Permissions Per File?

Okay, here's the issue I'm having and my (hopefully helpful) explanation of what's going on:

I have a folder I'll call Folder B and it's housed like this:

All Files > Folder A > Folder B (and all subfolders & files in Folder B).

The settings for Folder B are set so that anyone with a link within my organization can access it; however, each time I attempt to add items to Folder B, I have to set unique permissions for each item. In other words, the file permissions for Folder B do not "waterfall" down to the files.

I'd appreciate any help in resolving this!