Yes, Covidence takes a study-based approach, which means that you are encouraged to link references together to form studies where they relate to the same trial. If during import there is information available to link references then Covidence will immediately create study records for screening.
You can manually link references once they have reached the inclusion stage. Note, however, that merges cannot currently be undone! Furthermore, if data extraction has been started on multiple references, these cannot be merged.