Some aspects of the File Manager TAB are obvious, like the filters, but others are not ...
The file manager has a column called "assigned" there you will see 2 numbers with an icon,
-- one number shows how many items use the file inside "an image field"
-- and the other number how many items use the file inside a "file field"
CURRENTLY it does not show the usage of files by minigallery or other third party fields
NOTE: You should never delete images manually, because they may be in use by items. First edit items to remove all uses of a file and then you can select it in the file manager and click delete.
FUTURE enhancements / plans: