All versions of the file, saved by each user will be backed up. The backup will be saved separately on their own version. 

For example, if a file called MyDocument.doc exists in a server and we have 2 machines connected to the server and accessing the file (A and B). After finish modifying, A does a backup, the file will be saved as A -> Path\MyDocument.doc version 1. When B does a backup, it will go to B -> Path\MyDocument.doc version 1. When the server does the backup, the file will be backed up as Server -> Path\MyDocument.doc version 1.