If you are using the Connect integration, you can pay off multiple invoices in one transaction without having to run a separate payment for each individual invoice.
Go to Connect > Make a Payment in the left navigation bar
Select to search by Invoice Number
Enter the first invoice number in the search box
Click Search
Check the box on the left side on the results grid
Enter the second invoice number in the search box
Click Search
Check the box on the left side on the results grid
Repeat this process until you have located all of the invoices you want to applied to the payment.
Go to Show just above the results grid and change the dropdown box from Current Search to Selected
Now you should see the complete list of all invoices you specified
Click Next
Allocate the appropriate amount of funds to each invoice
Click Next
Either use Manual Entry to enter a new card/apply to an existing payer or create a Send for Payment link.