This will be calibrated and entered in the control software such as Mach 3, EMC, etc.
You take the lead of the screw. Say 5/16"-18. This is 18 threads per inch.
1/4"-20 is 20 threads per inch and so on.
1.8 degree steppers make 200 steps in one revolution.
Say we use 3/4"-10 rod. You have 10 turns per inch, so multiply that times the steps per rev on the motor. That gives you 2000 steps in an inch.
Most drives use fractional stepping or micro stepping modes. For instance, Gecko 203V's are 10th step drives. This multiplies the revolutions by 10, so that alone with the motor would give you 2000 steps per rev. Multiply that times the screw lead and you have 20,000 steps per inch.
You can have all different sized threads on each axis and different motors and even different drives as well as combinations of metric and imperial for each axis and still do fine.
You would just have to calculate each drive separately and enter them that way. Throw some belt drives in the mix and you have more calculations to do, but it can be done.
These calcs will get you close or perfect, but you should check the distances in actual use to make sure or to calibrate them. All this sounds kinda hard, but really it's fairly simple. Math isn't a favorite thing of mine and I managed it several times without breaking down in tears.