I'm glad you've reached out to the Community. I can help provide an overview of the Flat Rate Scheme (FRS) in QuickBooks Online (QBO).
When you run financial reports, it will always show that the VAT is calculated as 20% which is the standard rate. While preparing the VAT return, QBO will automatically use the flat rate you've set up once you submit the actual return.
You can pull up the Prepare Return report to show you the calculation of how much is your payable to the HMRC and your savings for the FRS VAT.
In the left tab, select Taxes.
Click Prepare Return.
For additional reference, you can always visit these articles to learn more about the VAT calculation: