Follow these steps:

1. Determine the appropriate microstepping for the system. The higher you go the smoother the motion would be, but you will start losing torque as you go higher. This will also demand more speed from the motion controller to keep up with the required pulse stream. For regular steppers on a router table 1/8 should be a good number, for a mill, maybe 1/16 or maybe even higher. You need to move the motors under load and check how they feel.

2. Determine the Steps per Unit. Now that you have a known number of pulses per revolution, and if you know the lead of the screw and maybe you have some gearing, you can do the math to determine the number of pulses you need. You can also command a known motion, then measure the error and correct the current value in the proportion of the error. Most interpreter programs have a tool for this. When doing this, make sure to have the axis moving in the same direction so that you do not include the backslash in your measurement. Keep also in mind that the longer the measurement, the higher the resolution.

3. Determine the acceleration/deceleration. This you will have to play with and has mostly to do with the mass that the motors are going to move. You do not want your machine shaking as it is cutting.

4. Determine the Max Velocity. Keep in mind that motors lose torque as they gain speed, so it is good practice to move the axes as fast as possible until you start losing steps. Check if there is anything you can do to optimize your hardware. Then set the speed lower to where you consider the axes can work reliably. I like to tune them down about 30% from the speed that I noticed it started losing steps.