Total Payments under the Payment Journal will include Fees and Taxes on those payments.

If you'd like to know how much you received after taxes and fees, you should use the Tax Report. This will show you all payments (Cash Report) or Projects with payments (Accrual Report) after fees, and you will see a total of Taxable Sales & Taxes.

To know how much you 'kept' after processing fees and taxes, take the Taxable Sales and subtract Taxes.