Re: I manually paid an invoice $5,376.00 and also matched a payment of $5,376.00 in QB Invoice is...
I'm happy to see you're taking full advantage of the features available in QuickBooks Online to make your life easier. QuickBooks comes with some advanced tracking for Accounts Receivable, as well as time-saving synchronization with your bank account. Using these features together provides you with powerful reporting, without requiring a lot of your time. In order to unlock the full potential of this, it's important to have your invoices and payments recorded accurately. I'm here to help your sort this out.
If the bank transaction was Matched to the existing payment, that signals to QuickBooks that they are the same. If this is what happened, you can leave things as is without causing any problems. If the bank transaction was Added as a new payment, it exists as a duplicate. You can resolve this in just a few easy steps (it's preferable to keep the bank feed transaction to make reconciling easier):
Head to the Sales menu then select Customers.
Find and open the customer for which you created the invoice.
You should see two payments of the same amount. Open the one you wish to delete (you can view Online Banking Matches in the top left of the Payment)
Select More in the footer. Then select Void or Delete.
Select Yes to confirm.
If you accidentally delete the payment matched to the bank feed, it'll return to the For Review section of your Banking tab. You'll be able to match it to the invoice from there. This article includes the steps and some additional information regarding deleting transactions: Void or delete transactions in QuickBooks Online