Hello @Lisa1151,
Thanks for posting in QuickBooks Community.
Right now, the automatic payment doesn't have an option to include an invoice number. If you want to know which customer invoices are for that specific payment, you can contact our Merchant Support Team. Doing this, they will be able to assist you in assigning it to the right invoice.
Let me know how it goes. I'll be here should you need anything else. Best regards
