How do I manually mark an invoice as paid?

It's a pleasure to have you in the Community today, @twoway. I've got your back, and I'll walk you through on how to manually mark invoice as paid in QuickBooks Online (QBO).

Before anything else, I'd like to congratulate you for choosing QuickBooks for your business. To manually mark the invoice as paid in QBO, you'll want to go to the Receive Payment section, which you can find if you click the +New button on the left navigational bar. I'll input the steps below so you can proceed. Here's how:

1. Access your QuickBooks Online company.
2. On the left navigational bar, click the +New button.
3. Under Customers column, select Receive payment.
4. Select the name of the customer from the drop-down menu.
5. Enter the payment method and the amount received.
6. Tick the box for the correct invoice.
7. Review the amounts under the Payment column.
8. Once done, click Save and close.

For visual reference, see the screenshots that I've attached. 

You can also receive invoice payments from the Sales tab and then the Invoice section. In case you want to continue with this method, I'll gladly input the steps below. To begin, here's how:

1. Access your QuickBooks Online company.
2. On the left navigational bar, go to the Sales tab.
3. Select Invoices.
4. Choose the invoice and then from the Action column, click the Receive payment button.

In addition, I've got you this article in case you'd like to customise your sales form to match your business here in QBO: Customise invoices, estimates, and sales receipts in QuickBooks Online.

You can also visit this page to learn more about how to track the money in and out in QBO: Track your cash flow in QuickBooks Online.

@twoway, If you need further assistance managing invoice payments in QuickBooks, don't hesitate to get back to me by clicking the REPLY button below. You can also post here again if you have any additional QuickBooks-related concerns. I'll be more than happy to help you out again. Take care, and have a nice day.