Incident light meters are used for BTZS which doesn't have you place readings on Zones.
Zone System uses spotmeters (or get up close) to find the reflectivity of each part of your subject. So when you aim at your indigo, the needle would drop. When you aim at the yellow the needle will go up. So then you might place the indigo in Zone III but the yellow would fall in Zone IV.
How color affects film versus how it affects your eye versus how it affects your light meter... Now that is an interesting issue that you generally dig into when you start working with filters. A yellow filter on your scene would make the indigo darker still without affecting the yellow much. So you might end up with indigo in Zone II and yellow in Zone IV.
...edit... Oh you're talking two different pictures. Yea, you might be wise to consider the color of your significant shadow. You might want to expose the two scenes exactly the same. Thus you place the shaded indigo in Zone III and you turn the camera and shoot the next shot without changing the aperture/shutter speed. (Or keeping in mind color, don't pick a lighter-color subject in your shadow as the significant shadow.)