A source system collects together a number of entities (and entity mappings), to declare that they can all be created by one system. The system is only identified by a reference; you can think of the "source system" as a group of related entities if you like (though in a configuration with multiple sources, it makes sense to have one "source system" per source system).
Like entities and fields, source systems have references. Simply link to all the entities/entity mappings that the source can send. (You only need to link to the entities if the source system writes data using the default entity names. The list of entities to be created in the database is specified in the release, which is covered later.)