If you look at the schematic for Controller Board 2.8, the information on the six auxiliary wires is mostly on Sheet 2, with a little more on Sheet 6.
The six auxiliary wires are attached to pins 20 through 25 on the main wire harness connector (a DB-25 connector). From there they go to six test points, labelled TP20 through TP25. If you hold the board in your hand with the DB-25 connector on your left, the test points are on the lower left side of the board.
Things are made more complicated by the fact that 5 of the 6 pins are pre-wired to attach external lights and an external servo. But the user has the opportunity to undo this pre-wiring, by removing resistors R70-R72 (located on Sheet 2), and R73 and R74 (located on Sheet 6). These resistors are located under the motor speed controllers (ESCs) that are soldered onto the board, so it will take a little finesse with the soldering iron to get at them. You can see a photo of where some of the resistors are in this forum thread.
So wires TP24 and TP25 are already pre-wired to +5V and ground, so you might want to leave those wires as-is. The +5V supply comes from the ESC BECs, and if this is not suitable for your needs you might want to remove resistor R71 and instead wire TP24 to one of the main +5V supply pins on the prototyping headers of the controller board. The other four test points- TP20 to TP23- can be made available for your use by removing R70, R73, and R74. After removing those jumpers, you can now run wires from TP20-TP23 to analog inputs on the microcontroller chip (Atmega 2560). There are spare analog inputs on prototyping header J4 - see Sheet 2 of the schematic for details.
Since you don’t say what your sensors are, I can’t judge whether the analog inputs on the Atmega 2560 are suitable for your application. If you really are trying to hook up a thermocouple, it will likely require some sort of amplifier/cold junction compensation before it can be routed to the A/D converters on the microcontroller.
If you’ve never done this kind of work before, this may all seem very complex and confusing. Take some time to study the schematics and carefully plan out what you’re going to do before attacking the board with a soldering iron. Then make sure you check your work carefully before applying power to the revised controller board.