You can report a No show to Booking.com from directly within the booking record in Caterbook. You can do this from the day of arrival, and up to 48 hours after the planned check-out date.
Once you've selected Yes and 'No show', you'll then have the option to apply any suggested cancellation penalty. This would also be reported to Booking.com. If you choose Yes here, the Caterbook 'Cancellation Penalty' extra will be automatically added to the booking, but you will still need to process a payment for this manually if one is needed.