If you are making one payment to a supplier for multiple invoices, you will need to add it as a supplier cash allocation payment.
To do this, click Actions in the top right
Select Cash Allocation
The following page will open to allow you to add your cash allocation payment.
Firstly you will need to enter the payment information
And the TOTAL amount of the cash allocation payment
Then select the invoices you want to pay off by ticking the check boxes and entering the amount of the payment you wish to apply to each invoice.
Once you have entered the information (you will not be able to enter more than an individual invoice is due, or enter less than the total payment amount), click Save