Multiple Materials

I'm going to start off with - I'm really new to this. I've been a programmer for years, but building a game in Unity and modelling in Blender, not much experience.

I started experimenting with a tile map [Hex], and so far, I've found Unity easy enough to use. Until it came to building a path. I attempted a couple of things, like giving each corner they're own material / normal, and all of that worked, but it was all connected to my base image (gravel). I didn't want to have to do a ton of work just for images to switch the base image. So I did a little looking and came across the multiple textures.

Now, my hex object doesn't have multiple sub meshes, but I read somewhere, that other people are attempting what I'm doing, so I continued.

Creating a preFab, I was able to assign a second material (cutout), and it applied correctly, and it ran with the image properly visible.

I then attempted to do apply the second material from code at runtime, and the it came out choppy (see image) - could someone explain why, or possibly point me in a better direction?

Thanks!