There are two relevant concepts you need to be aware of:
1) ACLs on files
2) parent attribute for a given file
(1) provides access for user X to file Z. It says nothing about where that file appears in the user's drive, if it appears at all. (the file will still be visible in 'Shared with me')
(2) by setting the parent to Root for a given user, or a particular folder that is already visible in that user's Drive, the file appears in that place.
It is possible (and somewhat strange to users only familiar with 'normal' files in Windows that appear in one and only one place) to have a single file appear in more than one place: just add additional parents to the file:
gam <UserTypeEntity> update drivefile <DriveFileEntity> addparents <DriveFolderIDList>
If you copy a file, a new instance gets created and you end up with independant files with identical names and stored (appearing) in two places, which is not the same as the same file appearing in two places.
--peter