Hi jowade
Thank you for posting.
For allowances that don’t sit into any of the main categories, assign them to Allowance – Other (but check this with the ATO). The best way to update this is to change the ATO category first in your Pay Items and then make a void pay for the employees affected. Once this is submitted, it will be updated on the ATO's side as well. If you have concerns about the category to assign, I would suggest reaching out to your advisor or contacting the ATO.
This Help Article, Assign ATO reporting categories for Single Touch Payroll, has more information on ATO categories that you can use as a guide.
Please feel free to post again. I'm happy to assist further.
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