I created two invoices in September and sent them to the customer.I realised I made a mistake and I deleted them,however they still got paid.How to allocate the payments?

Hi bretprew,

If the payment is valid, that will serve as a credit/unapplied payment for the customer and you can apply the payment to future invoice.

If you have issued a refund to the customer for the payment they made, you can record an expense transaction and match the refund from the bank transaction.

To record a refund:

1. Click on the + New.
2. Click on Expense, Add expense or Cheque. 
3. Select the customer you want to refund from the Payee ▼ dropdown.
4. From the Payment account ▼ dropdown, select the bank account where you deposited the overpayment to.
5. On the first line of the Category column, select Accounts Receivable.
6. Enter how much you want to refund in the Amount field.
7. Fill out the other fields as you see fit, then select Save and close.

To link the refund/expense to the overpayment:

1. Select + New.
2. Select Receive payment.
3. Select the same customer you used for the cheque or expense when recording the refund.
4. Fill out the other fields as you see fit.
5. Under the Outstanding Transaction section, select the checkbox for the Expense or Cheque you created when recording the refund.
6. Make sure the payment is equal to the open balance, then select Save and close.

You can also refer to this link to learn more about: Handle customer overpayments in QuickBooks Online.

Feel free to reply to this post if you have further concerns. I am around to help you.