A backup copies files in one direction: from the source to the destination.
A synchronization copies files in both directions: from the source to the destination, and from the destination to the source.
Intelligent Synchronization copies files in both directions, but it also keeps a history of where files were during the last synchronization. This allows for much finer control over what actions to take based on what has changed, and also allows it to detect changes such as the file only being modified in the source or destination.
It is advisable to use Intelligent Sync instead of the "old style" synchronization but note that SyncBackFree does not support Intelligent Synchronization.