You'll normally need a different Agent Reference number for each service.
For the CIS Online for Agents service you can use your Agent PAYE Reference if you already have one. If you don't then you can get one online from the Agent Reference Service. (Please note that there will be a delay of up to 4 working days between when you receive your reference number and when you will be able to complete your registration for CIS on the Government Gateway. This allows for uploading of your reference details onto the Government Gateway.)