you need only one microSD card with Linux image for Raspberry Pi 3.
The RTOS is the part of the hFramework library, which is uploaded every time you flash the new program to the CORE2 microcontroller - STM32.
Here you can find a tutorial that explains how to flash the first program (written in C++) to the real-time microcontroller: https://husarion.com/core2/tutorials/howtostart/run-your-first-program/