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Your comment made me realize that I simply need the tie the grounds together of the circuits using the same power source (battery pack) and NOT use a common ground for entire Bot.
You need to tie the grounds together for all circuits that that communicate with each other electrically, regardless of the power source. If you use optical isolation on every wire between the uC and the motor driver, then you would not tie the grounds between the circuits. But if there is even one signal that is direct(electrically) connected, the grounds must also be connected.