I'll share information about QuickBooks Payments, @APalozzi.

After your customer clicks the link, they will input their payment details as though they are paying an invoice. Once the payment is made, you will receive a confirmation email as well as a copy of the payment link sent to your email.

It will automatically link to an invoice from the customer. In the event of a partial payment, it will be linked to the oldest open invoice.

Lastly, after your customer submits a payment for the invoice, QuickBooks will handle the payment processing and categorization. 

Here is an article you can read to learn more about QuickBooks Payments: Receive and process payments in QuickBooks Online with QuickBooks Payments.

Let me know if you have questions about using QuickBooks Payments, The Community is always here to help. Have a great day.