You didn't state whether it was a payment received from a customer for 2 different invoices or a payment you are making to a vendor for 2 different invoices, so I will answer both options:
1) 1 payment received from a customer for 2 invoices - clic on customers, then click receive payment. Use the drop down arrow to select the correct customer. A window will open that shows all open invoices for the customer. Select the type (Cash, Check, Credit Card, etc) and enter the total amount of the payment. Select the invoices the payment is to be applied to and save.
2) Paying 2 separate vendor invoices with one payment - Click on the Vendor menu & select pay bills. All outstanding invoices for all vendors will appear. Scroll down and select the invoices you wish to pay. Even though you select multiple invoices, QuickBooks will lump them together into one payment (Check or Credit Card).
10 years experience as a QuickBooks user and Consultant