Never used a CNC shield myself, but the 3 pairs of step & direction pins are inputs to the CNC shield, which controls 3 stepper motors that drive the X, Y & Z axis. The direction pin controls the direction of rotation, clockwise or counter clockwise. The step pin usually accepts pulses. Each pulse causes the stepper motor to turn by 1x step angle. Changing the frequency of the pulses changes the speed of rotation. There's more to it but those are the basics.
There is usually software on the actual Arduino UNO shield that takes care of driving the motors via the CNC shield. The Arduino UNO generates the step and direction signals for all 3 (or 4) axis.
A quick search says that the software is called GRBL and you can get it from the github repository.
Note: You may get more input from other users if you get your question transferred to the Motors, Mechanics, Power & CNC section. One of the moderators may move it for you.
Output from the Arduino. Input to the Stepper Driver.
Set the x.dir pin to HIGH for stepping in one direction and LOW for stepping in the other direction.
Set the x.step pin to HIGH and then LOW to take one step. Repeat for as many steps as you need. Schedule the time between pulses to get the step rate that you want (within the capability of the hardware).
I don't think I explained very well, I'm sorry. These are the pins I mean that are on the CNC shield. Are these pins in the picture input or output or both?
If a person can use those pins as input, would I need an additional arduino board and maybe another stepper driver module to physically connect to those pins to send the signals? I've tried to find a place that explains how to use those pins on the CNC shield. But I can't find anything about those pins.
@mafokken , regarding your PM indicating you don't want my input:
but I was looking for help from someone with experience with the question I had.
I may not have experience with that particular board, but i know about stepper motors and how to drive them. I also know how to use google to search for a schematic for the board. Which is how i know that those connection points in your photo above are also signals that come from the Arduino UNO.
You don't have to believe or trust me or what @johnwasser has said.
I believe those are connected to the traces between the 'Arduino' OUTPUTs and the Stepper Driver INPUTs. Normally, they are not used. You can use them as outputs to monitor those pins (maybe add some LED's). You can unplug one or more of the stepper drivers and use them as general I/O pins. You can program the 'Arduino' to not use them and let some external device control your Stepper Driver.