Have a look at stepper motor basics which has a lot of background information.
I don't know what you mean by "microcontrollers" if they are different from your Unos.
A motor shield is a poor choice for controlling a stepper motor and AFAIK it will only control a single stepper motor.
If you want the two motors to move in sync it will be much easier if they are both controlled from the same Arduino.
You have not said what power supply you propose to use with your motors - volts and amps. You should not power any motor from the Arduino 5v pin - it cannot provide enough current and the Arduino may be damaged.
Generally speaking stepper motors are driven at a significantly higher voltage than their nominal voltage and the stepper motor driver ensures that they do not get too much current.
Post a link to the datasheet for the motors that you are using.