Thank you for reaching out to us, @mikehmoran.
As of now, routing invoices by payment type is not possible. Once your customer receives the invoice, they'll have an option to pay for it electronically.
Also, if your customer's payment is made using the payment link, automatically the invoices are paid inside QuickBooks Online.
If you want to pay using a third-party payment processor, then you'll have to manually record the invoice payments in QBO. Then you can also change the payment method on the create invoice page.
Please feel free to review this article for your reference: How QuickBooks Payments works.
If you have further questions, just reply to the thread. Have a good one!
