Taxes and Fees on Invoices are calculated depending on whether you have "This tax is Fee Exempt" selected or not for your Taxes.
For Fee Exempt Taxes:
The Subtotal = Pre-Tax Menu Item Total
Taxable Subtotal = Subtotal + Any Fees (like Gratuity)
Tax is only calculated on Menu Items with that Tax.
Fees are only calculated on the Menu Items with that Fee.
Taxes will not be calculated on any Taxes/Fees that are Fee Exempt.
For Fee Included Taxes:
The Subtotal = Pre-Tax Menu Item Total
Taxable Subtotal = Subtotal + Any Fees
Tax is only calculated on the Menu Items with that Tax.
Fees are only calculated on Menu Items with that Fee.
Taxes will be calculated on the total of any Menu Items with those Taxes and Fees.