Hello Peter,
You will need to go to the Government Gateway to adjust the submissions Clear Books is allowed to do on your behalf.
The VAT one is set up as you mentioned, but EC submissions need to have their own permission/authorisation.
Please can you go to the guide below. You will need to follow most of the steps as outlined as you did for VAT but this time, the service will be EC submissions.
http://www.clearbooks.co.uk/support/guides/vat-2/submitting-online-vat-returns/
Please ensure that your registered postcode and your VAT number in Settings > Organisation > Details are all correct before sending your submission.
Vanish