Invoicing is not working

I'd feel the same way if the system is not recording the transactions appropriately, @KH40_2 LCC

Since you're new to QuickBooks Payments, we'll deposit your first set of payments (sometimes referred to as a batch) within 5 business days for the first 1 to 4 weeks while your account is being set up. Once everything is good, you'll receive an email and we'll deposit payments considerably more quickly depending on the time when you processed the payment. See this article to learn more about payment deposit schedules: Find out when QuickBooks Payments deposits customer payments. 

On the other hand, referring to your client who paid the same invoice twice, click here on how to void or refund customer payments in QuickBooks Online.

Furthermore, if you've already received an email and the system is still not recording properly, you may want to contact QuickBooks Payments Support Team. This way, they'll be able to look at your account in a safe manner and find the root cause of this unusual behavior. Be sure to check their support hours to be assisted on time. 

Additionally, here's an overview of how to run all your open invoices and other financial reports in QuickBooks: Run reports in QuickBooks Online. 

I'll be right here if you have any invoice-related questions or anything you need assistance with. Just hit on the Reply button. Have a great day ahead!

@KH LCC 

Another option, sign up for a 3rd party merchant service to compare. You can cancel one of the accounts later or use it as a backup.