Supplier VAT only invoice.

Hello user50834, thanks for joining the Community. 

Recording a VAT-only transaction in QuickBooks can be tricky, but we've got the steps to create a 100% VAT transaction that will show in Box 4 on the VAT return:

1. Click on the + New button and choose Expense.
2. Either choose a payee or leave that box empty.
3. On the first line of the expense choose any of your Expense accounts.
4. For the amount enter a pound (1) and choose 20% S as the VAT code.
5. On the second line choose the same expense account.
6. For the amount, enter minus a pound (-1) and choose Exempt as the VAT code.
7. The total of the expense will show as 0.
8. Under the Subtotal box the VAT box will become editable.
9. Enter the desired VAT amount into the VAT box and Save the expense.

If you follow the example you gave, it still shows that I owe the supplier the VAT amount when I do not owe it, the factoring company has deducted the charge from our funds available pot, so we are not actually paying them anything as they have already deducted the amount of VAT from the money they need to pay us.

How do you account for the transaction then so the supplier account is 0.00 but it is on the VAT control account??