The Silhouette Studio software (V3.0 and higher) allows you to cut by line color.
You may select any line and go to the Line Color panel to adjust the line color:
After you have adjusted the select lines to the desired alternate colors, you may then go to the Cut Settings panel:
Here, you can select your cut conditions by the line colors present in the document. An example is shown below:
You can select the material type conditions for each line style by clicking on the color selection and then clicking on the desired material selection below.
If you desire to have the Silhoutte pause between line colors with different material conditions, you can select a material and right-click to "Add Pause". Doing so will add a pause after the selected material type so that the Silhouette stops before going on to the next line color option. This can be quite handy if you are desiring to cut different line color sets in different material types, or if you are wanting to define one line color to draw with a sketch pen and then another to cut out with a blade and want to pause between the two line sets.
If you desire to turn the line color off (so that it is not cut at all), you can un-check the checkmark box to the left of the line color in question in the Cut Settings panel.