One way: create a “bullet hole” splat texture in the terrain editor. Don’t paint with it for real, but do a test: set the brush size to 1 (or 2) and try to paint some bullet holes are certain spots. If that looks OK, then make the code paint it for you.
Look up how to read/change splat textures in code. When-ever a bullet hits the ground, redo those squares (set the bullet texture to weight 1, everything else to 0.) One old Q about this http://answers.unity3d.com/questions/128274/how-to-change-texture-on-parts-of-terrain.html