Reverse the Settings?


I just spent the last two hours trying to figure out why one of my programs wasn't working.  Know why?  It needs to have write access to a protected folder.  Makes sense when you say it that way.  But, on today's machines that can have hundreds if not thousands of folders, it can be quite a task to sort all those that need write access from those that do not. 


Is there an easier or more global way to be able to set folder/files in groups and then allow or disallow the entire group?  One way is to totally control all aspects of all one's software installs, but not all software allows control of defaults.  So, for instance, one may want to protect the Documents folder, and yet still allow access to certain subfolders by some programs.


Suggestions?