With our 9 Series Smart Transformer, it does NOT matter how the system is wired. You are able to zone the lights however you wish after the system is installed even if the lights are on different transformers.
With our Stratus and Mosaic transformers, it does require the lights to be wired in the manner you want to control them. All Zone 1 lights need to be wired together to Zone 1 on the transformer. Likewise for Zone 2.