Apply transparent texture to plain at runtime

I have an this model, it’s my character, it have only cubes, and, I need to dinamically texture these cubes with it cloth, so, I’ve placed planes attached to it’s body, and then I change the planes texture dinamically from code to change it’s accessories, but, the question is, is there a better mode to do this, and, how to apply transparent textures, textures with transparent background?

Character Model

Use a transparent shader.

    renderer.material.shader = Shader.Find ("Transparent/Diffuse");