Hi Mantova,
I appreciate your post. When you pay a bonus or commission, AccountRight considers the total gross pay as the regular wage of the employee and taxes it as such. This means you'll have to work out and adjust the PAYG withholding on the pay manually. For the current rates of PAYG withholding on bonuses and commissions, you can refer to the ATO's tax tables or consult with your accounting advisor.
There's also a useful article you can read that provides comprehensive information about how bonuses and commission payments are handled.
Please feel free to post again anytime you require further assistance.
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Kind regards,
Shella