Yes, you can pay multiple invoices using a single transaction. Please follow below mentioned steps.

1. Login to Client Area
2. At Home page, under Overdue Invoices, you will have an option Pay Now to make the payment for all due invoices.
3. or Go to Billing >> My Invoices 
4. You will get a button called Pay all on top-left corner to pay all due invoices using a single transaction.
5. You will get a single combined invoice for all unpaid invoices. Select the payment gateway from drop down, click on Make Payment button and proceed with the payment.