Where is the cold junction on the commercial thermocouples?
Your cold junctions (at least two!) are where you connect the two (different!) thermocouple metals to your circuit. Note that this can be in multiple steps, like: thermocoupe - connector - wires - PCB. These are all cold junctions. Keep them all at the same temperature and measure that temperature. If no heating or chilling effects occur that is simply the ambient temperature, and you can use a temperature sensor anywhere on your PCB, but it won't hurt to place it near the thermocouple connector and put heat-producing components as far away as possible.