If you are using Chroma as a Global effect, it will effect whatever color you have chosen on all the layers. However, if you use Chroma as an effect on the layer itself, it will only effect that layer.
As an alternative, if you are using still images, you could create a .png file instead of a .jpg. PNG files natively support transparency, so if the file is created correct, you can have the parts of it you want transparent without having ot use an effect.
