Modeling in parts or entire.

Hello, I am planning to make a model in Blender and import to Unity. There is a script that will change the color of several parts of the model. When building the model in Blender normally I use mirror so the parts of the model are integrated in the main model.
As the scripts will change the color of the complete mesh and the model is one mesh only I cannot get the desired effect. So my question is, do I have to build the model in separated parts and put all together without join them in the Unity?
The script uses a ray cast and box colliders, the project is to run in iPad. Any idea how to make it work?