What RIP are you printing with? Most Rips should (I thought anyway) automatically place/print the registration marks and send that data to the plotter when it's time to contour cut. For example (using our setup, JV3, Onyx 7.1, S160D):
1. Set up your file with a contour cut path specified (make the cut line an independent stroke named CutContour as a spot color)
2. Open and RIP as normal, being sure you use a Cutcontour quickset or your settings are set to recognize that spot color-assigned stroke as a cut-only element
3. Print as normal, Onyx automatically places the registration squares where needed, assigns an individual job number/barcode to the job and creates a CutContour file placed in a special predetermined folder (created when the program is installed)
4. Print is loaded in plotter, Onyx Cut Server is opened (Cut Server is part of Postershop but it's a seperate program that does nothing but contour cut printed jobs), and the job is opened by entering the barcode number printed on the job.
5. Upon entering the barcode number, your file appears, and you click cut now, The cut job is sent to the plotter, the plotter tells you place the knife head over the first mark, you do that, hit enter, and it reads ever mark, then cuts dead-on accurately.
Ever RIP I've ever used worked basically the same to one extent or another. If you're having to manually size and place registration marks at the design stage, create a second file from your design file that will be the cut file, figure out how to get the plotter to read/register those marks and cut that seperate file, I'd honestly suggest you upgrade your software. I remember way back in the day when we had a SummaChrome (made by Westcomp, before they were Summa, this was the original original Summa thermal transfer printer, probably 8-10 years ago) this is how we had to print and cut jobs, by creating two seperate files, manually placing reg marks and hoping to god it worked right. Technology has changed, it'll do all that for you now, don't even try to do it yourself, it's so inaccurate and inefficient you'll recover the cost of upgrading in time saved in short order.
