@Brandon29063 Thank you for reaching out to the QuickBooks Community for answers.
Since sales receipt transactions can not be linked to invoices, you can reference the invoice number that the payment belongs to by utilizing the memo box available at the bottom of the payment screen.

Sending payment receipts in-product would be a great feature and I would advise you to submit a feature request within the QuickBooks feedback option.
Did you know you can also send a payment receipt from the Merchant Service Center?
Here's how:
- Sign in to your payments account at merchantcenter.intuit.com
- From the home screen click Transactions.
- Filter transactions by date and click Search.
- Find the line item for the payment and click on the Gear symbol to the far right.
- From the menu select Email receipt.
Let me know if this works for you.