In my opinion there's two things you could do.
First, and possibly preferent, you could compare the date at which a file was last edited with the date of the file in your backup system. If the file on the machine is newer than the one in your backup system you need to back it up. If a file is not present in your backup system at all you need to back it up too.
Second, you could use a FileSystemWatcher
] to be notified the moment a file is created, updated, deleted etc.
How you are going to realize any of these (or other methods) is up to you.
Hope it helps! :)