I'm here with some information that I'm sure you'll find helpful regarding automatic invoice and payments, @cedarvalley.
QuickBooks Payments only allows one-time payment on invoices, either partial or full payment. When your customer gives you additional payments, you can enter them using the instructions below:
Once done, it will automatically update the customer's balance. You can refer to this article for more info: Record customer payment.
You can also take advantage of our Progress Invoicing feature. It allows you to split an estimate as many invoices as you need. Instead of asking for full payment, you can invoice customers for partial payments. To get in-depth information about this feature, check out this link: Set up and send progress invoices.
Please come back if you need further assistance in setting up the Progress Invoicing feature. I look forward to being able to help you again in the future.