Hi jcarafa
Sorry to see that no one has replied to you yet. My understanding is that Partner Pay is paid directly to the employee so wouldn't need to be recorded in your software.
For the top-up using Annual leave I'd recommend checking with Services Australia that this is permitted. If it is, it could be processed as normal, however, I would suggest checking this with the ATO or your accountant.
Please let me know if you need further help.
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