How can I change the tax settings in standard payroll for employee income like allowances? It automatically adds its own settings that are incorrect for what I'm doing.

Hi,
This is an interesting question. I’ll be happy to assist. With QuickBooks Online, you can add additional pay types to your employees in a few simple steps. That being said, editing the settings of additional pay types is not an integrated feature of the system.
To know more about the pay types available in QuickBooks Online Payroll, check this community article: https://quickbooks.intuit.com/learn-support/en-ca/help-articles/pay-types-overview/01/261579.
Let me know if you need help with anything else.