I'm here to help ensure your Profit & Loss (P&L) report will show the correct income tax, JR88.

You need to use the standard VAT codes on the actual transactions even though you've set up the Flat Rate Scheme (FRS). QuickBooks will do the calculation for you on the VAT return for the FRS.

For example, if you have sales or expenses, you should include the 20% standard rate VAT. QuickBooks will work it out according to your FRS %.

You also need to consider looking at the accounting method of the report. The FRS accrual and cash method will show different amounts

Here's a link for further explanation about this: QuickBooks Online Flat Rate Scheme explained. 

Don't hesitate to post again if you have follow-up questions about the income tax reported on the P&L report.