If you have recorded a payment coming into your bank prior to an invoice being raised you can later associate it to an invoice/receipt by going to Bank > View/Add Transactions > Selecting the transaction > Clicking the Assign to Invoice/Purchase button. You can also assign multiple payments to multiple invoices/receipts at once by going to Bank > View/Add Transactions > Use the tickboxes down the right hand side to select the transactions > Use the dropdown at the bottom to select assign to invoices/receipts > Click Go.