Hi there, pitchess.

Thanks for joining the Community.

I'm backing up my colleagues' information that paying a partial payment in QuickBooks Payments will automatically mark the invoice as closed or fully paid. As an alternative, you'll need to manually track the remaining balance and add it to your QuickBooks Payments account.

You can refer to the steps provided above of my colleague @Rasa-LilaM.

Once done, you'll need to select an option Need Invoice? to create an invoice. Then your customer can pay now the remaining balance.

To know more about creating invoice payment in QuickBooks, check out this article for future reference: Let your customers pay invoices online.

If you need anything else, please post a comment in Community. We are here to back you up. Have a good one!