With the new concept of surrogate (foreign) keys in AX 2012. We now use the RecId for setting up relationships.
If you wondered how it affects your filters in the query selection.
Below is an example of what it looks like. You will have both the RecId and the Primary key of the related table available for selection.
First time you select it it will look like this.It shows the main table and field name.
Next time you open the same selection. You will notice it has automatically established the relationship and changed the table and field in the query. Now it says People table rather than Department.