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Hi angusk572
You could create one payment within the VAT centre that relates to both of the individual payments you make, you will of course have to delete the payments you have created. The subsequent VAT period/payments will not have the correct amount displayed however once the credit has been used the period after that will show correctly, the VAT suspense account will also show correctly at this point.
or
Record the first payment as normal within the Taxes section
For the second payment: you can create a prepayment account (a bank account called pre-payments) and post it there, when you create the second expense select the bank account the amount was debited from as normal however in the category section select the prepayments account.
When the time comes to make the payment for next return you will use the prepayment account to make the payment accordingly, say if the next return payment is less than what you have in prepayment account
You will leave the difference in prepayment for next return payment