UK VAT flat-rate scheme

Have been reading this item with interest as i don’t seem to have a problem using manager.io for flat rate vat. All sales invoices are sent out using the tax code for 20%flat rate, and pay the HMRC our given rate which is 10% of the total (i.e. net + 20%vat). Since purchase vat is not included in the calcaulation it’s not recorded. I do only do book-keeping but the accountant receives all the paperwork at year end with a trial balance and seems satisfied. Do you think I am doing something wrong or I am just lucky it works for me. I wouldn’t like to have to manage changes that may upset this.