Well, let me say this first...It is hard to use up (98%) two n3 configured as you do, 32 in and 32 out, spread out as 16x16 each, you have me wondering what exactly is being done, so I would like you to call and talk it thru with us.
That said, there are no fast and hard rules about how best to configure your project, or how to best use the XDAB. Consider if you had two ballrooms, and so just a few inputs and outputs need to be shared across the XDAB, then 16 x 16 each would be a good plan.
But instead it could be a single large ballroom, then having the inputs in one NION going to mixers for each room, and then to a room combiner, then thru the XDAB to get to the output processing and out the NIO-8o cards in the other NION.
But a 32x32 could be a big conference room, with a little input processing, and then into an Auto-Mixer, and on to the XDAB. Next would be a big Matrix-Mix, with the last step being output processing.
If this was a new install, I would suggest testing (an emulation will show how much DSP and memory is used) a n6 with 4) NIO-8ML II for 32 inputs, and then 2) CAB 16o for 32 outputs.
So what's right? Well with NIONs and NWare, for every "right" way to do it, there are 5 other ways that are just as right.
Make it intuitive, never leave them guessing.