Set your registration marks in Illy using CuttingMaster. just make sure that once there set, there is enough space between the marks and the edge of your vinyl for the clamp wheels to ride outside the marks.
Save your file and relatively center the print on your vinyl. Do your lamination if needed.
Now, it is essential to get your stock square in the plotter. I found the the most accurate way to do this is to stick a thumbnail on both front marks and line them up with the groove in plotter bed. It sounds a bit awkward but I run full 50 yard rolls of printed sheets without ever have to re-register them.
Let the graphtec load the stock as usual than manually align the blade inside the corner of the mark closest to the blade using the arrow keys.
Open your file in Illy again with only your cut layer visible. Send the print under the "Advanced" tab in Cutting Master. The plotter will ask you if the cutting head is within the first registration mark. Hit OK and the Graphtec read all four corners and than cut your cut layer.
Other than the print this whole process is independent of Onyx.