You enter your sales at 20% as normal - the flat rate only applies when you do the return.
Suppose for the sake of simple numbers you’ve made £1,000 of net sales in a quarter plus 20% VAT. On normal VAT accounting your return tells HMRC “I’ve made £1,000 of sales (box 6) and I owe you £200 of VAT on those (box 1), minus whatever I’ve claimed back on purchases (box 4)”.
But on flat rate the return instead says “I’ve made £1,200 of VAT inclusive sales (box 6), and I owe you 10.5% of that total - £126 (box 1)”. The flat rate percentage applies to the gross total sales including VAT (at 20%), and reduces the amount you put in box 1, but in return you aren’t allowed to claim back VAT that you paid on purchases in box 4. QuickFile will adjust as part of the VAT return process to move the difference between the 20%-of-net that you charged your customers and the 10.5%-of-gross that you declared on your return back over to the “sales” section of your profit and loss report.
Any VAT invoices you give to your customers still say they were charged 20% VAT, and if they’re VAT registered (and not themselves on flat rate) they can reclaim that in the normal way.