Hello there, ronan.
You'll need to visit this website to verify the correct Flat Rate Scheme (FRS) rate: VAT Notice 733: Flat Rate Scheme for small businesses.
Once you have confirm the rate, I'd be happy to walk you through how to enter it in QuickBooks:
You can also check out the following articles to be more familiar with FRS and how it works in QuickBooks Online:
Let me know if you have more questions aside from this, please let me know so I can further help.
I know that we are a limited input company, so our rate is 16.5%, and I know where to set this. I just want to check that it's the correct figure to enter...as in, 16.5% is applied to the gross figure to work out what we pay to HMRC, so I'm assuming this is the correct figure to put into the VAT FRS rate setting in quickbooks?
I'm being extra careful as when I was doing the books on a spreadsheet and using the TMRC page to do VAT returns I made an error nearly every quarter!
(I had to turn off FRS on the system to amend something, and then turn it back on.)
If your FRS rate is 16.5%, then this is what you enter in the VAT settings. This will then be used to work out your VAT based on HMRC regulations - Box 6 x your flat rate = Box 1. Any reclaimed purchase amounts are then taken away from this figure to equal the amount due to pay.