Can I pay an automatic invoice with an external payment like a check?

Unfortunately, any automatic invoices that are created cannot be changed to manual or paid using the same external payment methods as a manual invoice. We would recommend closing the current invoice as paid and then writing a note on the Account Notes section of the customer's account detailing the manual payment for that invoice. Alternatively, you could also stop collection on the invoice and have it marked as failed, once that's done, you can move forward with creating a new one-time manual invoice for the amount owed and record the manual payment there.