Hi there, @aestheticheadpro.
I'm here to shed some light on how QuickBooks Payment works.
QuickBooks Payments allows you to accept invoice payments from your customers. Know that the invoices need to be created in QBO, so you can send them to your customers and have them paid online.
If the invoices for your website aren't created in the system, the merchant services account can't be used. You may consider using other options to receive payments for your website.
To give you more details about utilizing QuickBooks Payments for your sales transactions in QuickBooks Online, please check out this link: Learn how to receive customer payments for online invoices and in-person sales.
You can always get back to me here if you need help with payments or with QuickBooks. I got you covered. Take care!