Is there a way to link a bank payment thats paying multiple invoice amounts together to the separate invoices even when the total amount sent doesn't match invoice total

Welcome to the Community, @murphysbrisbane.

Yes, there is an easy way to link the payment to multiple invoices in QuickBooks Online. You can first create a Receive Payment transaction and apply it to all the customer invoices being paid. Then match that payment to the bank deposit in the Banking feed. This ensures everything is organized and prevents any duplicate entries.

Here's how to:

1. Click Create and choose Receive Payment.
2. Select from the dropdown arrows the Customer, Payment Date, and Payment method.
3. Choose Undeposited funds from the Deposit to dropdown.
4. Tick the check boxes for all the invoices the one payment covers. The total should match the bank transfer amount.
5. Hit Save and close.
   
   

Then go to the banking transactions to match the payment.

Here's how:

1. Hover your mouse over All apps, choose Accounting, then Bank transactions.
2. From the For review tab, locate the deposit transaction. Click Match and choose the payment you created.
3. Confirm the match.

This way, the invoices are marked paid, the bank transaction is matched, and reconciliation stays accurate, with no duplicates or double-counting.