The Many-To-Many Relationship can be used to store a relation between 2 Business Models.
For example if you have a model "Person" and a model "Car" and a "Person" can have multiple "Cars" and a "Car" can be assigned to multiple "People" you can use this relation to easily find the "Cars" a "Person" is using and the "People" who are assigned to a "Car".
You can specify filters which will be applied when creating/update objects and when filtering.
For example if the model "Person" has property of type Status(Active,Not Active), you can set a filter in model "Car" - Person.Status In Active.
If you do this users will not able to create/update of filter objects of type "Car" where the Person.Status is not Active.