I've worked with GL_TEXTURE_3D a lot lately, I might be able to help. But ... I just don't understand what you're trying to do.
Can you try to clarify what is your goal ?
Anyway, if you already know that you only have 3 layers, input 3 Sampler2D to your shader, it's gonna be fine.
Most of the time, I use Texture_3D only for textures like 256x512x1024 pixel, that can't be passed as 256 Sampler2D.