When you are ready to submit your regular CCC copyright payment order, see Submitting Copyright Orders. This will pay all of the CCC copyright items that had copyright recorded in version 6.5 or higher of the ILLiad Client. Once payment is complete for the CCC copyright items, run the Copyright Web Report (under Administrative Reports) to see a list of the remaining transactions for which copyright payment is still outstanding. These will display in the top section of the report: Finished Requests with Copyright Fees. These non-CCC copyright transactions should be easily identifiable by the CCCNumber note added during copyright processing.
Submit payment according to whatever process is necessary to do so. Once copyright has been paid for these items, add a note to the transaction record (example: 'Copyright paid to Publisher') and mark the record as Copyright Already Paid in the Item Information pane.