I can share some information about recording invoices, @PNRA.
Regardless of the format that you're using, if your customers will now pay the invoice that you've sent to them, you'll just have to record an invoice payment to mark it as paid. Here's how to receive and record invoice payments:
Go to the + New button and choose Receive Payment.
From the Customer drop-down, select the name of the customer.
Select the payment method from the Payment method drop-down.
From the Deposit to drop-down, select the account you put the payment into.
In the Outstanding Transactions section, select the checkbox for the invoice your recording payment for.
Click on Save and close once you're done.
After you process a payment, it'll now mark the invoice as paid and keep your accounting system balanced.
This connects the payment transaction to the original invoice so your accounts stay balanced.
QBO is unable to separate Proforma Invoice and Commercial Invoice. Some of our clients are having an additional app to integrate with their QBO accounts. They will issue a Proforma Invoice before the goods have been produced or delivered and a Commercial Invoice to the buyer after the goods have been delivered or shipped. The commercial invoice confirms the exact quantity of the products that have actually been loaded and shipped. They may ask buyer to countersign the Proforma Invoice or Customer Invoice by the system if required.