NHibernate ManyToMany relationship that includes all of one side of the relationship

Answer 1

I think the best way is what you've already suggested, to map each table as an entity. If you didn't have additional data in the join table you wouldn't need to, but as you do they should really be separate entities.

You'd have three entities. Facility and Compliance would have a HasMany to Facil_Compliance. You'd also have a References from Facil_Compliance back to each table. You may optionally remove a direction from this relationship if you only ever need to go one way.