Invoices can be paid using the allocate button or the record payment method. If either of these two methods are used, the payment is not automatically reconciled on your bank account.
The bank explain screen allows you to reconcile paid invoices with receipts. The bank explain screen can be reached from the Manage money options or via an imported statement.
This guide demonstrates how to reconcile a paid invoice with a receipt on an imported statement.
Navigate to the Money > Bank accounts menu.
Scroll to the bottom of the screen where you will find a table listing all imported statements that need explaining.
Click on the Explain link for the bank statement that you would like to begin explaining.
Click on the appropriate receipt that you want to reconcile with a paid invoice.
Select the customer in the From box.
A table with recent transactions will appear as shown in the screenshot below. Any paid invoices that match the amount of the receipt will have the option to reconcile under the Add column. Click on the Reconcile button.
Once the invoice is reconciled the transaction on the imported statement will be marked as explained and the statement for the account will also mark the deposit as reconciled.