Creating a cut here is much like creating a cut in illustrator. The only difference is not only does the layer need to be named by the cut name (Through Cut), but you need to make the stroke a spot color that is named "Through Cut" also. The system picks up the spot color in the PDF and converts it to a cut. See the screenshot for the details and adding a new swatch. To get to this panel open the swatches window and click on the options in the upper right hand corner and click add new swatch.