You use the longest table travel to set the steps per unit. See ALT 6 page lower left hand corner and use the axis calibration feature of MAch. Any inaccuracy in the step setting is a very small amount in a short move as compared to the steps required for a long move.
Since the screw lead may vary over it's total length, ie; ball screw specs sometimes are over some distance and thus the lead error may not be not be linear over that distance ie; more in one section as compared to another. For a short distance ie; 1" you can use a dial indicator, preferably one in 0.0001" resolution.
Now if you could, which I have done opticaly, you can actualy profile the screw and see how it varies in both directions.
You have what you have and then must deal with it.
As far as measuring something, well it all depends on what you have available to do the measurements with.
RICH