You will need to go to check in desk for the airline which is stated on your itinerary.
In some cases your flight may be operated by another airline. This is called a 'codeshare'.
If you are travelling on a codeshare flight you will need to go to the desk of the aircraft which is operating the flight. For example, if you have a Qantas flight from London-Melbourne but it is 'operated' by Emirates you will need to go to the Emirates check-in desk.
Please also check the screens at the airport for check in desk information.