If you haven't linked to an accounting platform (Xero or MYOB) you will need to manually mark your invoices as paid.
You can also follow these steps to clear out an invoice that hasn't been paid by a few cents.
First, find your invoice either in the Payments column of the status board or through Search:
You can also use the Invoices Due report in the Reports menu to find your invoice.
Then click Payments:
Fill out all the fields and click Add Payment:
Marking multiple invoices as paid
If you want to quickly mark multiple invoices as paid, open up the Customer Invoice Report and tick the box beside each invoice you'd like to mark as paid, and then click Mark selected as paid:
Have a payment from your customer with reference Promisepay? See this article: Reconciling Fergus Pay deposits in your accounting package