Hello Community users, we just wanted to stop by and add an update to this thread, with the resolution for the original post.
When you add a percentage discount to the customer invoice it will not discount on the VAT percentage as well. This is how the QuickBooks product was designed. You can amend the VAT amount in the VAT calculation box if the rounding pence does as it may round up/down slightly on a transaction but you can not give a percentage discount on an invoice that will impact VAT.
Any questions just ask.
