Your flight reference can be found on your invoice/confirmation. This is not your Thomas Cook booking reference. Your flight reference is in the flights section of your Thomas Cook invoice and labelled Airline reference, an example is shown below, obviously, your reference will be unique to your holiday. You will need this reference to check-in online and add any flight extras such as baggage and pre booked seats.
If you need help with online check-in, we have created some guides for some of the most populate airline to help. You'll find them in the Airline Check-in section.
Airlines can sometimes refer to this as a PNR if you need to talk to them at all.