Here's what I do to fine tune the motors after the velocity and accel has been dertermined (see other post for that good advice).
I started with the rough calculation for steps per inch. In my case the math worked out to 4000 steps per inch.
So I entered that (4000) into the X axis "steps per unit" box.
I then set up a dial indicator and issued a command for the X axis to travel one inch (after I had manualy taken up the backlash...get to that later).
After the travel stopped I read the dial indicator and it indicated 1.012 inches of real travel.
Here is where the "fine tuning" comes in. take the previous "steps per unit" (4000) and divide it by the 1.012 inches of real travel = 3952.57. This is the NEW value that I enter into the "steps per unit" for the X axis.
I repeated the above process several times until I got it to repeat dead on the money every time. I then duplicated this process to the Y and Z axises.
Now for backlash. rotate the lead screw to remove any backlash. setup your dial indicator and comand your system to move by .25 or so in the same direction. Then command the machine to return to zero. The dial indicator will show you your backlash. Repeat this a couple of times to be sure. Then you can enter that value for the particular axis under the "backlash" under the config dropdown menu. Be sure to also ENABLE BACKLASH under Config/State/Backlash ON option.
Repeat this for all axises and you should now be pretty well setup.....