Hello Castle,
You don't need to record the payment that didn't auto-post to the invoice. Let me provide you with insights on how it flows in QuickBooks.
Estimates are non-posting transactions and do not impact any income or revenue reports. When a customer pays for an estimate and deposit online, it is recorded as a liability because the work has not commenced. After the estimate is transformed into an invoice, the deposit is applied to the total invoice amount and then recognized as income.
For further information and details about the required deposit for estimates, please refer to the following article: Request a customer deposit on an estimate in QuickBooks Online.
To enhance your QuickBooks experience, consider collaborating with our QuickBooks Live Expert Assisted team. These financial professionals specialize in streamlining processes and providing tailored advice to meet your business's unique needs.
After your customer has approved and accepted the estimate, you can convert it into an invoice. For more information, please refer to this article: Convert an estimate to an invoice.
Please don't hesitate to revisit the Community if you have further questions or concerns regarding your estimates and invoices. We are committed to providing a prompt response.