First, you need a low level VI that accepts an integer number of steps and in response moves that number of steps. To implement that you need logic that sends the bit pattern required to make one step to the motor over and over again. So yes, you want a 2D array of booleans that controls the outputs to step one time. To make multiple steps, replay the array multiple times. If it were me writing it I would use nested loops. The inner loop performs the transitions need to do one step, the outer loop calls the inner loop for each step requested.
Important! Don't forget that you are dealing with a mechanical system that has mass and inertia. There is a maximum rate at which you can step the motors. Be sure to include delays in the inner loop to ensure that you don't exceed that limit.
Your second question is if I step a given nimber, how do I know if I'm where I am supposed to be? You need some sort of feedback. You need a sensor to tell you where you are. The most common way is to use a stepper motor with a built-in encoder.With that you can tell the motor to move and then read the encoder to see if it did.
If you don't have some way to tell where you are it's not the end of the world. Just remember for your next project you need motors with encoders and limit switches to tell when you have reached the limit of your axis travels.
Or better yet, next time spec three of those really nice stepper motors with built-in controllers and serial interfaces. Then you can tell the motor to step N times, and it just does it.
Mike...