Structure of folders/files in games directory

[FizzyMUC]

Hi folks,
I've been setting up this little gem yesterday and with my first test it seemed to work well, up to the point when I put my game files and the DLCs, updates into subfolders. Now it does not show me the directories or the files. Is there a special structure I need to use so everything works? I was just thinking that the file browser could be a bit crowded if I have game files, update files, DLC files and saves all in the same generic games folder. Does anyone have a nice method for this?