Powering Trinamic TOS-100 separately - 5V Pin concern

I have an Arduino Mega 2560 being powered from a 12V DC source....the Trinamic TOS-100 board is stacked on top of the Arduino. However, it needs to control a stepper motor which requires 9V-12V....so I have another set of power jack cable going to the Trinamic. On top the Trinamic is a custom board with components used to measure input analog readings from an LM35 temperature sensor. That sensor is being powered with the regulated 5V coming from the 5V on the custom board.

Is that actually the case? In terms of the bottom Arduino's regulated 5V making it's way up to the custom board?

If I power the Trinamic board straight from the supply, does the 5V pin on it do anything, or just "pass" the voltage up to the custom board?