No matter what you do, you can not reprogram each of the ECU to match the keys you have. If one is reprogrammed with your keys, the other ECU will then not match the keys you have.
You will need two sets of key fobs, or, if you have two key fobs, get one programmed to match one ECU and the other to match the other ECU. It's not the key that is reprogrammed, but the security chip in the key fob. This includes the security chip in any of the keys that didn't include the remote (supplied before tow remotes became standard in Aus).
How do I knnow this - well, from experience. When we got the second remote key, it had to be programmed, along with the existing remote key fob. As we didn't have the key without the remote in the car, it was not reprogrammed and would not start the car.
Then, we had a security chip fail. The secirity chip was replaced (not the remote, just the chip in it), and all three keys were reprogrammed. Now all keys work, including the non-remote.
Sorry to add further problems to your bright idea.
Bob