I'm not certain I understand. Are you saying that the hidden folder does not appear after you unhide them or that after you unhide them that the copied files don't appear?
The process should be to unhide the folders, copy the files, and then paste them into the folders as listed in the ReadMe.
C:\Documents and Settings\(your account)\Application Data\MakeMusic\Finale 2014
This is a path to where the folders are located so that you can copy files from the template package and paste them in the correct locations.