There are two methods for referencing Marks. There is the Reference Mode which is entered into using the Reference Mode and Pane and there is the Quick Reference command.
Quick Reference is used when only a one or two objects need to be referenced, whereas the Referencing Mode is more useful when a number of marks have to be referenced together. Referencing Mode can also drive you through referencing (mark by mark) so there is less chance a mark will be missed (i.e. remain unreferenced). Quick Reference though does have the advantage of being able to select objects from Tables, Projections, and the 3D Viewer for referencing.