When receiving a payment, it is considered a best practice to always match the payment up with the corresponding open invoice. That said, from time to time, you may notice an unapplied payment sitting on a customer's account. To link the unapplied payment to an open invoice, open the payment in QuickBooks and apply it to the open invoice.
Open the unapplied payment in QuickBooks
Select the applicable invoice(s) from the Outstanding Transactions list
Sync QuickBooks and Novi (optional)
If you have an urgent information change that must be done in QuickBooks, you can do a manual sync in Novi to bring over the information. This is done by clicking the "Sync Manually" button at the top right of the admin section in Novi (circled below).
However, you don't need to do this for every little change, because QuickBooks and Novi sync throughout the day. A full sync of QuickBooks data occurs between 12AM - 5AM EST and a partial data sync occurs two times a day between 10AM and Midnight EST.
Additional Info
More information on how and when your Novi data and data in QuickBooks sync.
If credit memos are automatically being applied to open invoices and you would rather issue a refund (or vice versa), refer to this QuickBooks Online help article for steps to edit your settings.