Hi, @newbchip. I can direct you to a website that offers a variety of tools for applying payments to invoices.
Please know that we cannot suggest a third-party app that enables matching payment to its specific invoice in various transactions under a parent customer or account. However, you can look for a tool that will help recognize which one corresponds to the other. To proceed, check out their features and user feedback on this link: Apps for QuickBooks Desktop.
Additionally, QuickBooks Payments supports accepting payments through credit cards, debit cards, ACH bank transfers, PayPal, and Venmo. If you're interested in exploring, refer to this article: Take and process payments in QuickBooks Desktop.
Furthermore, you can generate summaries of customer invoices, payments, credits, and balances associated with the parent and the sub-customer moving forward: Create and send customer statements in QuickBooks Desktop.
Swing by if you have follow-up questions about managing invoice settlements. I'm more than happy to assist you. Have a great day!