I think I’m starting to get this! 
My only question (and I’ll leave you alone after this) is why have both the logic and motor ground connected to the Barrel Jack ground? That’s 12v input, so shouldn’t the logic ground come from the 5v Capacitor ground?
It’s so much easier on a breadboard when you have different power and ground rails! Haha. I never really thought about the ground and power too much in a more permanent situation. It’s confusing!