With any combination of circuitry that is switching high currents and logic circuitry, having the same 0v rail is not a problem as long as it is wired correctly. You need to ensure the 0v currents for the motor do not run though your logic 0v otherwise you'll have major problems. Having a 'star' point for your 0v wires is a good start - your logic 0v, motor 0v and power supplies 0v all meet at one point.

Stepper motors are mechanically simple but electrically complex devices to drive. Everyone wants lots of torque and speed but that can be difficult to achieve. You need to give the coils lots of current to step and a lower current to hold so you don't smoke the motor. Chopper drive is the best, but to design a chopper drive for a reasonable sized motor is a challenge as you're switching high currents at high frequencies and that requires careful design of the circuit board and the circuitry. In some instances it is easier to design a dc servo motor control - at least then getting lots of torque and speed is relatively easy. I would suggest you get an old HP inkjet printer (should be pretty easy as most people upgrade inkjets almost weekly!). These have a combination of stepper and dc servo motors in them so you can have a look at the circuitry they use to drive them - especially the steppers.