Thank you for your response Ekaterina! Sorry I didn’t get a chance to come back to this till now. My samples are exactly in the shape you described above (8x8x12). I used OHE for twice the number of pieces to accommodate for the 2 colored pieces.
Can you please give more pointers on “use some layers that can make sense of the relative positions of the pieces on the board instead of flattening the input data?” I’m sure this is my key problem. Any examples would be greatly useful. Are there any existing models that I could reuse at all?
The other two links/papers are not quite useful for my problem since I’m not really trying to recognize chess images.