When I draw a stacked area plot using Matplotlib's stackplot, if a set of y values has a negative number in it, then that area will overlap with the area underneath. For example:
import matplotlib.pyplot as plt
plt.stackplot([1,2,3], [1,2,3], [1,0,-1])
plt.show()
You can see the top set of y values are in orange. Since the right most y value is -1, it overlaps with the blue region. This is fine for my purposes. Except, I need that to be clear it's an overlap as opposed to the blue region just stayed at y=2.0 from x=2.0 to x=3.0 and the orange area is positive. Can overlaps like this be set to a different color?

Yes, you could draw the second y data in two runs:
I think, however, a better solution would be to make the colors semi-transpartent, maybe with additional hatching: