If your agency processes a payment on your insured's behalf utilizing either your insured's checking or credit card directly on the Carrier, MGA, or Finance Company site, this is a Direct Bill 100% entry in your NowCerts management system. Therefore, there will be no Accounts Receivable to invoice and no "issue payment" to retain your commission. There is only your agency and agent commission tracking, and likely the Carrier or MGA site will allow for a receipt.
If you want to create an agency receipt for such actions, go to Documents > Invoices/Receipts > Take Payment Options. Either "take payment" for a one-off receipt or "quick payment" for a one-off or from a list of invoices. Check it out, let us know if you have questions.