what rip software are you using?
For me I use Flexi/Production Manager. I set the contour around the image then in the printing set up under the advanced tab I click on the contour button and select the cutter you will be sending it to, make sure that the media width is the same in this window as it is in the print setup, decied how you want the registration marks to print and send as seperate jobs to the production manager.
After it is done printing load it in the cutter and on the cutters menu display select mark position, and use the arrows to line up the blade with each of the regestration marks.
Then on the production manager click send on the job and it should ask about the alignment, again line up the blade on each of the registration marks and you should be good to go.
I don't know if that makes sense or if you can follow that, but that's how I do it with my Falcon.