From your client area, you are being given a way to automatically pay tall the invoices at once even if they aren't merged into one.
In order to proceed, you would need to login to your client area and go to the "My Invoices" section.
From your invoices list, you'll notice in the sidebar a Pay All button which would merge all outstanding invoices and prompt you to the payment gateway choice.
That's it, you'll able to clear all outstanding invoices at once following this simple step.