First load the printed vinyl making sure it is as square to the plotter as possible. I actually press my thumbnails on the registration marks and move the vinyl until both ends drop in the groove on the plotter bed. Close the clamp and let the plotter register the vinyl width.
Next, using the arrow keys, move the plotter knife in the center area of the closest registration mark. Don't do anything else like setting the origin or anything.
Re-open your file in Illustrator. Hide all the layers but the cut layer and the registration layer. I don't think this is supposed to be necessary but for some reason, my Cutting master will cut all visible vector lines if I don't.
Open Cutting Master and make sure your graphic is in the same direction on screen as it is in the plotter. If not, cancel, go back to Illy, unlock everything and rotate it as needed.
Go back to Cm and send the job. You should get a warning box that basically asks if you have the knife lined up in the registration mark. Click OK and you plotter should read all 4 marks and than cut the image.
I printed and cut 2,000 decals last week. I set them up in sheets of 28 and printed them in 5 sheet runs. Once they were in the plotter I sent them as 5 sheet multiples and ran the whole 150' roll without ever repositioning the vinyl.