Ok this image shows that I have two contour lines. The one on the inside is tough to see because it is inside the black outline. The color of the inside contour is gray and the color of the outside contour is red.
Here I have the cutting window open in the Rip/Print menu. You can see that I have two drawing colors.
Here I have clicked "edit" and I'm going to assign a condition to the gray path. I have also unchecked "use same driver options for all colors"
Here I have assigned a different condition number to the red contour.
So from here, you just have to edit your conditions on your cutter to the settings that you desire. For the red contour line I have my condition set to perf cut. When you have finished all of this, you will be able to send the job from production manager, it will cut the entire job with the first condition, then it will ask you to switch to tool position 3, and you can continue with your perf cutting.