Increasing the depth of the holes should get them to show up on your cabinet. You'll have to play around with the entered depth to get the actual dilled depth that you're looking for. Once the holes do show up, the depth shown in the ecabinets nest diagrams should be the depth that you end up when you do drill them.
For one of my angled cabinets, I had to enter a drill depth of 18.96mm to get the holes to display, and drill at 9.5mm.