There are 96 TCIP6B595 outputs. The last pin on the headers connects to Vin or to 5V, jumper selectable.
The TCIP6B595 are daisychained and supplied by SPI.
So one shifts out the cathode data for all xx cathodes and the anode for that layer. With 20mA LEDs (really bright!) you'd need 1.82A of current with 91 LEDs.
9 refresh cycles for 9 layers.
Or maybe do 1/2 of the layer, then the other half of the layer, and just need 1A of current. 18 refresh layers. Still have to shift all the data for the whole layer.
The remaining '328 IO pins are broken out near the '328, with a couple driving 2 transistors, or one can leave the transistors out and jumper across them.
The analog pins have +5, GND near them, the remaining digital pins have Gnd near them.