If you need to process a payment for a bigger amount than the one you have on balance, you can book a trade for the difference and then just send a payment from the Payment section.
For further assistance, feel free to contact Ebury support directly via live chat or at the below email addresses:
EMEA (operationsteam@ebury.com)
Asia Pacific (operationsteam.apac@ebury.com)
America (operationsteam.ca@ebury.com)