This can be an amazingly hard to find piece of documentation. I spent about 2 hours tonight trying to find the right words to put into Google to discover it.
It seems like what you are TRYING to do is add an item to a collection, delete an item from a collection, or save changes to a child collection in your entity class. However what you really want to do is manually manage the link table.
A useful additional thing to document (this is deducible from the "How Do I" but not necessarily obvious) would be How to delete a m:n relation between two entity objects:
DepartmentEntity department = new DepartmentEntity(1);
department.DepartmentEmployees[0].Delete();
ps. I know you know the documentation could use help. I'm mainly noting this here in hope of helping google find this for the next guy.