Post a link to the datasheet for the thermocouple amplifiers.
This is the link to the amplifier -> Adafruit Universal Thermocouple Amplifier MAX31856 Breakout : ID 3263 : $17.50 : Adafruit Industries, Unique & fun DIY electronics and kits
This one for the teccnical details -> Downloads | Adafruit MAX31856 Universal Thermocouple Amplifier | Adafruit Learning System
Two extra pins next to AREF on UNO R3 are SDA, SCL (they have label on bottom side) and they are the same as A4, A5 so it is same if you will use A4,A5 or these. It is I2C bus. The reason why they are on two places is just to have same position for I2C on each board even with different MCU
I don´t know what I2C means (or MCU). Does this mean I can use them as an I/O pin?